[English] 日本語
Yorodumi
- PDB-7orb: Crystal structure of the L452R mutant receptor binding domain of ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7orb
TitleCrystal structure of the L452R mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-75 and COVOX-253 Fabs
Components
  • (COVOX-253 Fab ...) x 2
  • (COVOX-75 Fab ...) x 2
  • Spike protein S1
KeywordsVIRAL PROTEIN / SARS-CoV-2 B.1.1.7 variant / B.1.351 variant / P.1 variant / B.1.617 variant / antibody / receptor-binding-domain / spike / neutralisation / VIRAL PROTEIN/IMMUNE SYSTEM
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhou, D. / Ren, J. / Stuart, D.I.
Funding support United Kingdom, China, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 China
CitationJournal: Cell / Year: 2021
Title: Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum.
Authors: Liu, C. / Ginn, H.M. / Dejnirattisai, W. / Supasa, P. / Wang, B. / Tuekprakhon, A. / Nutalai, R. / Zhou, D. / Mentzer, A.J. / Zhao, Y. / Duyvesteyn, H.M.E. / Lopez-Camacho, C. / Slon-Campos, ...Authors: Liu, C. / Ginn, H.M. / Dejnirattisai, W. / Supasa, P. / Wang, B. / Tuekprakhon, A. / Nutalai, R. / Zhou, D. / Mentzer, A.J. / Zhao, Y. / Duyvesteyn, H.M.E. / Lopez-Camacho, C. / Slon-Campos, J. / Walter, T.S. / Skelly, D. / Johnson, S.A. / Ritter, T.G. / Mason, C. / Costa Clemens, S.A. / Gomes Naveca, F. / Nascimento, V. / Nascimento, F. / Fernandes da Costa, C. / Resende, P.C. / Pauvolid-Correa, A. / Siqueira, M.M. / Dold, C. / Temperton, N. / Dong, T. / Pollard, A.J. / Knight, J.C. / Crook, D. / Lambe, T. / Clutterbuck, E. / Bibi, S. / Flaxman, A. / Bittaye, M. / Belij-Rammerstorfer, S. / Gilbert, S.C. / Malik, T. / Carroll, M.W. / Klenerman, P. / Barnes, E. / Dunachie, S.J. / Baillie, V. / Serafin, N. / Ditse, Z. / Da Silva, K. / Paterson, N.G. / Williams, M.A. / Hall, D.R. / Madhi, S. / Nunes, M.C. / Goulder, P. / Fry, E.E. / Mongkolsapaya, J. / Ren, J. / Stuart, D.I. / Screaton, G.R.
History
DepositionJun 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 18, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entity_branch_descriptor / pdbx_initial_refinement_model
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
R: Spike protein S1
H: COVOX-253 Fab heavy chain
L: COVOX-253 Fab light chain
A: COVOX-75 Fab heavy chain
B: COVOX-75 Fab light chain
X: Spike protein S1
C: COVOX-253 Fab heavy chain
D: COVOX-253 Fab light chain
E: COVOX-75 Fab heavy chain
F: COVOX-75 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,81344
Polymers237,77910
Non-polymers6,03334
Water7,512417
1
R: Spike protein S1
H: COVOX-253 Fab heavy chain
L: COVOX-253 Fab light chain
A: COVOX-75 Fab heavy chain
B: COVOX-75 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,70520
Polymers118,8905
Non-polymers2,81515
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
X: Spike protein S1
C: COVOX-253 Fab heavy chain
D: COVOX-253 Fab light chain
E: COVOX-75 Fab heavy chain
F: COVOX-75 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,10824
Polymers118,8905
Non-polymers3,21819
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.239, 149.425, 115.040
Angle α, β, γ (deg.)90.000, 92.025, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "B" and (resid 1 through 3 or resid 5...
d_2ens_1(chain "D" and (resid 1 through 3 or resid 5...
d_3ens_1(chain "L" and (resid 1 through 3 or resid 5...
d_1ens_2(chain "C" and (resid 1 through 45 or resid 47 through 224 or resid 300 through 401))
d_2ens_2(chain "H" and (resid 1 through 45 or resid 47 through 224 or resid 300 through 401))
d_1ens_3(chain "R" and (resid 333 through 345 or resid 347 through 516 or resid 600 through 702))
d_2ens_3(chain "X" and (resid 333 through 345 or resid 347 through 516 or resid 600 through 702))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel seq-ID
d_11ens_1ASPGLNB1 - 3
d_12ens_1THRPROB5 - 8
d_13ens_1SERSERB12
d_14ens_1SERSERB14
d_15ens_1GLYGLYB16
d_16ens_1THRTHRB20
d_17ens_1CYSGLNB23 - 27
d_18ens_1SERSERB31
d_19ens_1LEUGLYB33 - 41
d_110ens_1ALAPROB43 - 44
d_111ens_1LEUTYRB46 - 49
d_112ens_1SERSERB52 - 53
d_113ens_1GLYGLYB57
d_114ens_1PROPROB59
d_115ens_1ARGSERB61 - 76
d_116ens_1LEULEUB78
d_117ens_1PROALAB80 - 84
d_118ens_1TYRGLNB86 - 90
d_119ens_1SERSERB93
d_120ens_1PROPROB95
d_121ens_1THRGLYB97 - 99
d_122ens_1GLYLEUB101 - 125
d_123ens_1SERSERB127 - 162
d_124ens_1THRALAB164 - 193
d_125ens_1GLUGLYB195 - 212
d_21ens_1ASPGLND1 - 3
d_22ens_1THRPROD5 - 8
d_23ens_1SERSERD12
d_24ens_1SERSERD14
d_25ens_1GLYGLYD16
d_26ens_1THRTHRD20
d_27ens_1CYSGLND23 - 27
d_28ens_1SERSERD31
d_29ens_1LEUGLYD34 - 42
d_210ens_1ALAPROD44 - 45
d_211ens_1LEUTYRD47 - 50
d_212ens_1SERSERD53 - 54
d_213ens_1GLYGLYD58
d_214ens_1PROPROD60
d_215ens_1ARGSERD62 - 77
d_216ens_1LEULEUD79
d_217ens_1PROALAD81 - 85
d_218ens_1TYRGLND87 - 91
d_219ens_1SERSERD94
d_220ens_1PROPROD96
d_221ens_1THRGLYD98 - 100
d_222ens_1GLYLEUD102 - 126
d_223ens_1SERSERD128 - 163
d_224ens_1THRALAD165 - 194
d_225ens_1GLUGLYD196 - 213
d_31ens_1ASPGLNL1 - 3
d_32ens_1THRPROL5 - 8
d_33ens_1SERSERL12
d_34ens_1SERSERL14
d_35ens_1GLYGLYL16
d_36ens_1THRTHRL20
d_37ens_1CYSGLNL23 - 27
d_38ens_1SERSERL31
d_39ens_1LEUGLYL34 - 42
d_310ens_1ALAPROL44 - 45
d_311ens_1LEUTYRL47 - 50
d_312ens_1SERSERL53 - 54
d_313ens_1GLYGLYL58
d_314ens_1PROPROL60
d_315ens_1ARGSERL62 - 77
d_316ens_1LEULEUL79
d_317ens_1PROALAL81 - 85
d_318ens_1TYRGLNL87 - 91
d_319ens_1SERSERL94
d_320ens_1PROPROL96
d_321ens_1THRGLYL98 - 100
d_322ens_1GLYLEUL102 - 126
d_323ens_1SERSERL128 - 163
d_324ens_1THRALAL165 - 194
d_325ens_1GLUGLYL196 - 213
d_11ens_2GLNLEUC1 - 45
d_12ens_2TRPLYSC47 - 219
d_13ens_2FUCFUCK
d_14ens_2NAGNAGK
d_15ens_2NAGNAGK
d_21ens_2GLNLEUH1 - 45
d_22ens_2TRPLYSH47 - 219
d_23ens_2FUCFUCI
d_24ens_2NAGNAGI
d_25ens_2NAGNAGI
d_11ens_3THRTHRR2 - 14
d_12ens_3PHEGLUR16 - 185
d_13ens_3FUCFUCG
d_14ens_3NAGNAGG
d_15ens_3NAGNAGG
d_16ens_3BMABMAG
d_21ens_3THRTHRX1 - 13
d_22ens_3PHEGLUX15 - 184
d_23ens_3FUCFUCJ
d_24ens_3NAGNAGJ
d_25ens_3NAGNAGJ
d_26ens_3BMABMAJ

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.0397443543125, -0.518278706158, -0.85428775541), (0.747466356071, 0.582803875273, -0.318800391324), (0.663109668789, -0.625880839865, 0.410559059635)-12.1821581268, -20.0873455804, 54.8038184461
2given(-0.0393972562223, 0.516699011843, 0.855260186939), (-0.744731461299, -0.58584409381, 0.319627514928), (0.66620035031, -0.624346721709, 0.407882660012)-34.3094949044, 20.6326702404, 54.8004206694
3given(-0.999997752018, -0.00159666361347, 0.00139521475503), (0.00160143085217, -0.999992861141, 0.0034224387721), (0.00138974031133, 0.00342466541847, 0.999993170121)-46.6559008608, 0.390092394799, 0.0603829155069
4given(-0.999937821641, 0.00996265634159, 0.00500982348177), (-0.0099409797036, -0.999941198109, 0.00433327218936), (0.00505269979633, 0.00428320020005, 0.99997806197)-47.0432028268, 0.237541580187, -0.0638984804296

-
Components

-
Protein , 1 types, 2 molecules RX

#1: Protein Spike protein S1


Mass: 23194.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2

-
Antibody , 4 types, 8 molecules HCLDAEBF

#2: Antibody COVOX-253 Fab heavy chain


Mass: 24371.400 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody COVOX-253 Fab light chain


Mass: 23256.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody COVOX-75 Fab heavy chain


Mass: 24821.846 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody COVOX-75 Fab light chain


Mass: 23244.861 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Sugars , 4 types, 4 molecules

#6: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#7: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#9: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

-
Non-polymers , 7 types, 447 molecules

#10: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#11: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#12: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#13: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#14: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#15: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M BIS-TRIS pH 6.5 and 16% (w/v) PEG 10000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 2.5→75 Å / Num. obs: 108845 / % possible obs: 99.8 % / Redundancy: 28.1 % / Biso Wilson estimate: 54.63 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.3 / Rpim(I) all: 0.058 / Net I/σ(I): 5.6
Reflection shellResolution: 2.5→2.58 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 5144 / CC1/2: 0.609

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
GDA1.19_4092data collection
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BEN

7ben


Resolution: 2.5→73.67 Å / SU ML: 0.4227 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.743
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2513 5504 5.08 %
Rwork0.2128 102853 -
obs0.2148 108357 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.47 Å2
Refinement stepCycle: LAST / Resolution: 2.5→73.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16134 0 391 417 16942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002416908
X-RAY DIFFRACTIONf_angle_d0.559522981
X-RAY DIFFRACTIONf_chiral_restr0.04292608
X-RAY DIFFRACTIONf_plane_restr0.0042915
X-RAY DIFFRACTIONf_dihedral_angle_d12.28016118
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2DX-RAY DIFFRACTIONTorsion NCS1.50051822445
ens_1d_3LX-RAY DIFFRACTIONTorsion NCS1.46293208506
ens_2d_2HX-RAY DIFFRACTIONTorsion NCS0.288943806319
ens_3d_2XX-RAY DIFFRACTIONTorsion NCS0.47660012684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.36941390.35462805X-RAY DIFFRACTION80.75
2.53-2.550.37371990.3543418X-RAY DIFFRACTION99.81
2.55-2.590.40121910.34283428X-RAY DIFFRACTION99.92
2.59-2.620.38871600.33513456X-RAY DIFFRACTION99.94
2.62-2.650.34972000.31683422X-RAY DIFFRACTION99.92
2.65-2.690.34161750.30093459X-RAY DIFFRACTION99.92
2.69-2.730.33892040.28813402X-RAY DIFFRACTION99.92
2.73-2.770.32111910.283402X-RAY DIFFRACTION99.94
2.77-2.810.30281880.26673470X-RAY DIFFRACTION99.97
2.81-2.860.32261700.26053454X-RAY DIFFRACTION99.92
2.86-2.910.26791490.25113471X-RAY DIFFRACTION99.92
2.91-2.960.3091640.24823447X-RAY DIFFRACTION100
2.96-3.020.30391610.2493487X-RAY DIFFRACTION99.97
3.02-3.080.29461840.24663433X-RAY DIFFRACTION100
3.08-3.150.26331850.24613443X-RAY DIFFRACTION99.94
3.15-3.220.31312030.24363432X-RAY DIFFRACTION100
3.22-3.30.30152080.23183409X-RAY DIFFRACTION100
3.3-3.390.26821550.22393472X-RAY DIFFRACTION99.97
3.39-3.490.24051800.21413466X-RAY DIFFRACTION99.97
3.49-3.60.23451690.21143475X-RAY DIFFRACTION100
3.6-3.730.26481870.20273466X-RAY DIFFRACTION100
3.73-3.880.24492110.20013387X-RAY DIFFRACTION99.97
3.88-4.060.22891620.18873486X-RAY DIFFRACTION100
4.06-4.270.20882100.17613436X-RAY DIFFRACTION99.97
4.27-4.540.20181920.16093442X-RAY DIFFRACTION100
4.54-4.890.20062230.1593432X-RAY DIFFRACTION100
4.89-5.380.18881920.15643453X-RAY DIFFRACTION100
5.38-6.160.23051740.18123472X-RAY DIFFRACTION100
6.16-7.760.21711890.20743500X-RAY DIFFRACTION100
7.76-73.670.23971890.21123528X-RAY DIFFRACTION99.68
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.43248610052-0.551010083041-1.41904373014.01421050387-1.212987988536.47272491390.0451275731220.567677831022-0.256494285935-0.634625187929-0.434891231056-0.296203242130.253376063550.8755324237780.4338804973160.472731552482-0.07777631963140.06886801728840.6236939214750.08023611491290.82792963688420.91636.04524.121
21.708210954130.853409046077-0.1774812182874.68234747979-1.407799409664.21536641988-0.00113883210788-0.2547912586110.5377248832140.2455989945-0.385313082668-0.350826608405-0.6354849713510.5590579702640.2689812374280.577198212429-0.195056326455-0.06247138630850.506966873407-0.0188928150020.82928179883315.38143.64530.061
31.007217433730.5514921576580.03339933497641.85128731167-1.729406878322.284462925030.207278006976-0.273781973053-0.1808750897410.251030494811-0.218452109926-0.0101883272679-0.1289240235480.4088417223150.1717164146330.475930591094-0.136403064580.0413782599350.436381653-0.06885331261050.6632181818285.08324.15340.214
43.005452263811.28300625297-0.2832721108883.66255782589-0.0007897231371192.86118062108-0.5298825672240.4512484705690.4370976032940.2045671166220.03936310897450.331758902179-0.6402302311450.2750364149260.202322958180.503793648336-0.0456065393654-0.01957730860590.315925273277-0.03809917674550.7804351315566.38436.75726.274
58.260623699361.456621790441.376865270551.489928021940.02643050421174.82727801923-0.208252466080.3514445153391.05232816409-0.1898974832290.3801064624330.0249711847953-0.95144275894-0.104085180946-0.1699178086050.602437762452-0.09665760030860.1434322426580.3686879602810.09816367521140.771317503517-27.4428.48438.669
63.76133061804-1.94856938173-0.01996589927741.01749538314-0.1846824818735.54751220074-0.157510442327-0.007128493396071.04991643606-0.4016577865330.1592922209730.0811106151807-0.308940017785-0.02901394725320.05752259671950.449079061656-0.06619109860230.1316433927560.3412302855960.01123547368050.677195383298-19.04322.47842.947
76.37757423153-0.7791408658780.8337259199480.833708560943-0.7844593617514.16743100830.05560373014720.3573454526190.405041110712-0.0352949316663-0.0174446550262-0.04065573267-0.205967495239-0.1961365731-0.07759289002940.481157352274-0.1006857808040.1011405141010.309785967337-0.003172950325150.54408027019-18.32922.69339.96
83.93832626005-1.19375272688-0.3748224803251.560742498271.44167448483.954927203960.1362522910320.1625816931721.345294415110.1110938752420.2627700235550.508635748271-0.3324705843470.248982537782-0.4289935953520.566553674127-0.07132096053650.09793985118250.464016889380.05496021080170.948947769312-51.22623.90447.147
94.11321359201-1.3586952207-0.01401564123213.650533171781.815675170497.17493470723-0.01891043776880.001620866890850.850156385840.205663324438-0.1570214947930.538382554763-0.872555091112-0.5009619626580.05917744759760.6417510193020.005925147604540.1424179034120.468252118985-0.08702500656521.02330500504-55.76328.90651.734
107.34978004025-0.737189609273-2.092215143212.94897914553-0.4699187038780.6947666107680.0883225228502-0.365937382122-0.106836687740.298767207582-0.125975186389-0.241506496871-0.02802201960930.0699263458401-0.03386372225420.495005630875-0.0461763054058-0.04256979155040.4432946902590.009043160522480.391262349456-21.9375.25157.688
114.12690417133-1.376419303380.1851570557772.21875314221-0.06802822563294.18335506008-0.0160566922131-0.7189615192130.4686125144470.7271155760980.01968345981770.0141685855118-0.310698244787-0.118438191759-0.03921211536050.5667974374-0.2164986759850.1049315725040.492454837562-0.1390218270430.504734438132-17.87415.05960.102
127.89090366664-0.191306732031-0.06926817310611.08426259614-0.4594123075760.225898160498-0.0531788517941-0.5154172389480.9555604529260.1767324024490.03290136727270.206734430313-0.295209747321-0.05857133274260.07119315578170.503026995655-0.07837874662010.1171875107260.457870092588-0.1446889628180.681490673364-37.12113.82755.451
136.958870968690.4191650274242.833918158621.26052300555-0.8342258341096.91872658354-0.0355117171521-0.1229822904890.09095204573590.1219354656260.2399619686780.466384706039-0.0499908496596-0.31159784747-0.1946014110670.4261640110330.004851358829160.1258758884120.44321395017-0.06566351495080.787698189491-56.1118.90451.102
142.524025034812.041043170770.7694839024242.915250057982.160347226832.57411513980.222831076459-0.2957605768510.2248710100190.217266898379-0.07862407349540.739067526531-0.128860124167-0.852871008477-0.248854530990.3107893816860.07569627401450.06772498916340.418768835908-0.01034980667290.651248556989-17.7847.9322.609
156.11118807182.578938808544.208083967075.243013040842.382474630982.95807147360.430872117811-1.016401208570.3222035660640.867752045865-0.8151423123091.187023079680.600410369716-1.03102244330.3904737493140.450592025604-0.0889793880460.1044857930660.489367050467-0.166272038930.633992455699-16.07510.53616.14
165.00445623321-0.12305397339-0.09533461863043.659987776791.838466320657.69341296552-0.0441981410182-0.113435505030.407233199708-0.202577932691-0.2854520954330.895930771091-0.57134830774-0.4526290925280.1249232517110.340945015524-0.0128911404908-0.02620474045990.308595472663-0.1093847885110.612664167319-13.3417.4088.196
171.016163127191.512864389822.719815489031.593924831582.881916685276.748299788660.0141694436222-0.04701417407750.110303390943-0.0249218786814-0.00212418777690.0501676897897-0.281996452955-0.2448174895330.1096565958320.2772178655180.03797480421310.003074448431720.350460247295-0.04897977597140.516404204573-9.66412.3146.493
184.88929928322-1.06002770704-1.049388682014.423950631730.6560766672733.87839345140.1575616325740.699398710083-0.307503122562-0.274461066287-0.151630248305-0.7180563925580.4869866480510.3920276058610.01069969240470.3222895431910.0703501321653-0.02736132335330.4253691039-0.1072753412810.479426199175-4.006-10.314-17.602
192.0216292242-4.48491193094-5.779770010676.380467451542.915105108633.07482926849-0.06859367532490.293514203598-2.1186424244-0.0146936413123-0.4429031853130.00831190268836-0.02841553307290.115224904356-0.3112328181140.5440712806730.0744842488886-0.04123803374220.599390773058-0.1182798309460.373808802172-12.677-13.381-17.665
201.19162207863-0.033142533754-1.212924622164.676735800180.8347880122663.890694125080.1128996629930.398216297664-0.236216958184-0.3576459617990.003244755139890.0992698444435-0.2232418144450.598784614732-0.1566027850350.301500552811-0.083229069877-0.05599123473330.453987483578-0.01897843669310.52559649352813.4599.3194.106
212.66357201699-1.37278703517-0.6795255204745.429528714740.844958730433.445837213410.104341486977-0.1059056746090.1562218139360.01238135336570.0709340865927-0.727665756978-0.2954908212180.529653593061-0.189278346210.295648634988-0.05000312961890.002344843300690.417798488262-0.08498443509760.4849870840318.43410.82812.898
226.02592048694-4.98046275962-0.9782816706145.21187756786-0.692237790582.978113900540.1629292491620.531136185106-0.2208806866050.275116665739-0.2974267582150.8196740335290.4016721847280.1545401959210.03724739624960.442439601701-0.0245876618415-0.07854644510920.393998528047-0.1603893849820.6422127686129.0553.3448.564
234.55571499177-0.13281223137-0.6529765450313.279071540222.016049279882.39511125767-0.20191746549-0.0322262611286-0.1426780281110.1815417271330.5905923625090.07537631157880.06754438458630.889403300012-0.3557778301640.3485672981770.00307268204344-0.08801699580860.46250431619-0.02535461566550.347344216958.5947.4811.399
249.30070736139-3.681576253823.022032732535.46289025056-0.2611272349829.017059064660.6382334054841.83635116444-1.04410808721-0.750652013744-0.179671808158-0.1067327043760.6954562001440.0167993766862-0.199545478770.422727078216-0.02064449440910.09134777449790.889664914607-0.2056214999830.467417337004-2.842-7.726-28.775
255.03959223161-1.347760095952.055189380473.727726247810.3493615258428.03558354617-0.08362037105930.6770956326981.06366036923-0.1767977766750.346424838337-0.7762823655690.18367977190.642124403557-0.1555022086440.3525014910160.01311284567290.06588904124880.743316642532-0.07097516755480.5721523767898.205-1.746-19.95
263.490993536422.409123022782.517062397316.94536634096-0.7408012443056.82103769095-0.05843301619151.030380635731.13844658322-0.9395306815920.116685605686-0.513296130033-0.7700105051741.462864067060.2059617025240.557263271469-0.03701201063250.09736089644250.8767926370310.2138105336160.9337971207215.0884.469-25.389
274.57386620486-0.2565888531160.656676479512.03083363427-0.2853446174393.264789410170.1314474783741.201560796940.028266833689-0.2384456474350.269913183461-0.22770009432-0.3980648281190.759324506834-0.3038205604110.4283391897670.05400219374180.09168713893321.04528304628-0.1317946878360.606375471476.941-3.859-24.553
282.369515542781.476743883970.2897570789835.664964808521.916937715762.92978937971-0.032421181610.131641232101-0.130949358324-0.681176377369-0.4208192528910.848645959071-0.0563637449109-0.6533791463390.5372928101960.526635548565-0.1059299792480.07332520954680.563976281442-0.0948195017560.924331432866-67.221-40.08624.015
293.105088805751.249230175580.3419405591353.963551955651.810425741552.96301681684-0.0056970075981-0.120906561327-0.8185169054980.350507911287-0.3821316582710.2106603714230.661120948693-0.4709873474180.1810607189180.583522815677-0.2106712880.131732136860.47129296964-0.02676930231170.850590121014-59.753-42.98432.38
303.008572824381.5040500025-0.9914895798862.031345650460.3644064741522.470466662620.279224217167-0.2852423292720.03620201410850.121680924064-0.2611401847340.1093764919220.290340151097-0.5523874635310.01910533524820.384499224578-0.05767492505940.07128475576090.321783842830.04540935632850.686687378021-53.501-25.939.248
312.41232508793-0.221422782937-0.2148712615380.1742385609030.1381067952854.50255521786-0.261926050929-0.0903043891346-0.07432320268180.0450834065999-0.1335430880740.4650063972790.2229111207160.171150186430.1521994686770.37301491614-0.1013489295160.0777246559840.2705020626740.03174731411080.696022230585-50.518-29.19233.116
326.631687367671.29369529032-0.7173585590292.4597347062-0.1901073135614.60654412614-0.254763140590.294467838146-0.851382750213-0.1407505604730.08983388922520.3880874047670.776839650056-0.1697839932720.1198271589180.459412990567-0.08428002900890.01602921234830.26821829741-0.05546462164380.63411061496-25.15-27.13741.14
338.247602310391.59541961584-0.7822697701924.84380378599-1.694144296854.81656593703-0.06924948542070.5212780309240.0125736501903-0.02891836476450.01994216315910.288585949269-0.01667344216750.355803412447-0.06541281331140.442585051002-0.102246231268-0.01614400409210.354960786778-0.01064656861040.436440841461-28.985-19.85437.529
345.836160227550.7855793399810.6485020130271.444506133820.1160572242410.655809570679-0.01848660915330.551701899149-0.1940428943230.1342609932620.0820272387206-0.171313638976-0.04788535031610.1309630560380.1036424777310.476865154951-0.0885251671019-0.000909503406750.34428297946-0.007086881984620.539869920794-16.147-22.68343.918
357.494306147991.20428353813-1.042424368572.41553035248-1.031258009465.16319894166-0.0908882728098-0.545105533277-1.246046058490.1224976023830.122497475068-0.4923113032010.705203755987-0.286924161227-0.03518755979990.509505148821-0.0191150827763-0.0008035572259840.4791386629120.110239742170.7862628653436.25-25.79150.255
363.661764179250.6459416792362.637282497052.9346483115-1.006295363712.50776591516-0.385266566918-0.731950127724-0.5954119730250.3118830093660.8788177127280.122145183853-0.78324959292-0.260179459746-0.135558146280.4903106621810.02373252565440.04032842117640.652899432044-0.06647889040050.537117315116-20.719-5.66659.023
374.926958547761.34178626986-0.5567098185512.415631116710.6137039419841.968098333850.303876880098-0.348046114908-0.04450503034930.27262429158-0.2740169832240.1631801606940.07940524011330.0226955308235-0.07657542951080.396793027339-0.1083527522860.03789396298690.3666480549660.0348953569370.369397181313-27.634-12.08956.038
385.381483826550.9366938182090.2609562615431.908371681180.5230841600592.354882186530.0833471995094-0.874966824771-0.6454058748460.8593174358130.1467348557220.7076624171930.138189875643-0.200242677833-0.05590574508610.648750252926-0.1044123850290.0746658287620.616893558630.06235737427940.470835327319-30.926-12.58563.37
397.212186451320.909162927448-0.936966532621.940344002620.6105277497470.6459727901080.312027451054-0.732521936174-1.704338274150.432568688677-0.253070468040.2880336478090.5149630460390.777715373760.07775549835530.556832694324-0.103970022874-0.01539532005730.5440174125520.1564508599670.648077795529-20.923-14.34162.202
406.85124497135-0.0576310000377-0.8102246960311.225229003110.5743908985140.947684991496-0.0360978338448-0.589942379066-0.4060892423350.1996093657260.05285977088440.157600191858-0.03673915278310.3027658847290.05522857847920.447881386126-0.165392629412-0.009128063027160.4499982630350.06941014065530.430278133551-17.784-9.22556.476
417.886146852710.393000163892-1.354008737883.046952203770.4908794407383.199593001050.093819459440.488672407233-1.8267111995-0.1700512075690.387648676188-0.7671013503880.5547038783220.4294346940440.2209252646330.459053541677-0.04737456813790.08330805876990.701883018713-0.1029981998781.2151679085116.134-18.13846.147
428.031605004620.331122618444-3.559509287293.674498741041.010361645117.235419375140.179772269556-0.1394483100640.3451670141030.4694707848530.1814900398-0.216900266158-0.251399656845-0.00382049200118-0.2824089451380.442411853018-0.1136478301860.04188293556350.6555258847260.07821533015010.5310256710626.629-8.19852.953
437.822389005571.92683039154-2.66114216972.58336011733-0.1328000633217.07029772151-0.233213699434-0.220713809781-0.08203227668980.3937110172180.329887305564-0.2937606686520.16776562223-0.482385860858-0.178689237790.5270611154140.134138230089-0.02045059577850.4947959553240.02025741935750.6554614553082.884-10.09252.947
447.58758832529-0.307617327748-1.912189868742.267786010691.592764990013.871074335750.1937625731190.826157888617-0.592505626681-0.09665890601380.0518488315518-0.865778848177-0.536711349910.100397608829-0.1722276812580.507332006597-0.06561705374540.06332299695030.630843191579-0.01128223290990.80128280693315.565-8.59344.108
457.77277220811-0.062843400434-2.330622720343.112516652951.182589625285.085905312410.665985991084-1.363882404280.13731936216-0.4645122812680.0384950854634-0.793579769371-0.9605255545391.67265872145-0.3105570139710.517154622357-0.0745196485584-0.1201691198530.9463800826420.02990789205180.74163636533515.455-5.43355.741
463.10916966552.288556171670.8513476374722.67737135893-1.539007697825.617056851930.235716981198-0.1917617841340.3030688680370.0682905737889-0.0743108973855-0.887372833099-0.3893442507890.14792666293-0.3454146615920.3087446497240.0426014270093-0.07827390292590.333796797441-0.06648530615290.657982882092-28.885-7.6072.63
474.34481125731.47199845342-3.217910848256.09923690041-0.245453535322.471761955440.460362942254-1.08332528377-0.02682735666560.803346281252-0.455300974822-0.851055165284-0.6602497472581.845849223540.008711102081890.457819083332-0.13525066028-0.07908825701470.6268893880310.09647792136030.507544831078-30.63-10.1916.172
484.17505996111-0.565572184868-0.8295665464524.12397406286-0.916720398937.33413675689-0.0904806893406-0.17314376009-0.671536063572-0.00116620877174-0.132568402472-0.473025813590.4911074042360.4364791390240.1795352728060.324136460115-0.01452545769550.04547852151630.3493605643940.1161946915130.536090904595-35.294-18.2587.274
493.674387801460.311856260078-1.338746902962.2427446659-2.549185387268.305734500580.141999290146-0.117672217931-0.4519802862510.0491910442287-0.331592242081-0.744271107080.1357546066940.3044044471170.1920076986350.292573433442-0.00552327634277-0.007911049576360.2961280847790.0905552007480.523024598486-31.267-13.3185.452
502.763519763760.758905765327-2.422487474441.7900375641-0.2622180606883.27907973047-0.000307151595420.128659655030.3328214144250.07995016460360.1682146511710.147958787498-0.319697643373-0.545884783294-0.04746007228020.3382295715670.0218029280495-0.05884161054920.3039561429310.04343599064420.543026955866-41.435-13.42517.754
513.55817602642-0.897882588669-0.1624155921942.847345660510.06348793412772.19436609159-0.09613203558930.447060922490.360034086404-0.05358363869160.1402275729610.46074731922-0.0827351249019-0.2283593778730.004273159242690.3143671516940.05514166688940.01835248860120.4342773102110.1231642855850.433754331269-39.4186.315-16.939
523.46133701381-0.05477481315620.7807364144713.920231700381.33491998674.27672092181-0.01948358061240.4268826825420.929011551274-0.011871348632-0.5181846722710.607331795694-0.978891866357-0.557915308440.1602543128750.4557345381390.1529369336620.05899294835030.5082355248660.1078262998170.863295181032-46.30616.316-18.933
534.88255763942-5.103748765412.511601418145.30547460958-2.615509879242.174552484730.06205104307360.6507643052660.6425764079260.448646490271-0.4261787115410.0837426535893-0.415419518990.0647253981980.2818514485930.3975415922970.004138548683650.004495699619420.3800927101780.04688529885070.400470309281-33.32111.485-14.445
547.20590329911-4.2353163446-1.248442628886.251366261121.063535901180.2490286224650.3957757750450.6906502698481.17360368643-0.601870083034-0.3568635311320.1846541789160.4484749530620.306735371648-0.2123276610370.540861672109-0.00594781701639-0.05600855630470.5566408247740.2550121688020.384063471529-34.76815.429-21.229
550.755103023797-0.991780897810.9532535041846.52078813496-0.590369709233.279342718960.04449888466940.264256082001-0.279281135673-0.0440108468059-0.104309886770.7287238544690.36978615208-0.7262194760620.1788853140720.339205969631-0.1095117405840.0779008757680.484371215890.06133209316510.538852745511-60.141-9.1294.096
564.29032106071-1.116745253370.3042158657213.29802467978-1.394253761325.403218942250.0168087135638-0.186154489957-0.1912405308440.03071754565190.2641083104050.5438373119660.112673916596-0.779776631774-0.2755643484970.291461300656-0.01002478634840.02722752288840.3553268726660.06566624895210.48837735881-55.1-10.58612.865
575.80535602784-2.92697294150.9297365119135.00690957153-1.586032866474.959132845350.3015233677460.5019990010750.441663422520.318465546507-0.234744636497-0.240165098411-0.490029257153-0.241519325953-0.05994656279940.424977883616-0.006059387685260.1170182453750.4882092943810.1844181820570.668217318911-55.74-3.1188.486
583.75512858549-0.4190884204761.200864901261.8862396195-2.093933575984.2772504801-0.09300001901660.1969586144920.115412264042-0.1655768652720.4720400955870.182804953810.123224937245-1.0642948731-0.3756635245150.376733060294-0.0320607733820.1056855864160.4677861859530.03825977655210.57678456682-55.257-7.3031.337
593.72745980306-3.15724389039-3.52041282375.19269552110.6631539962637.576550367130.194388731141.00988005270.890154143489-0.4874018027070.1169940089790.0329572354446-0.0069372465078-0.104496619187-0.2268931482530.461637636106-0.0198855698609-0.04240222668680.9091990790250.1661606428490.383946877062-43.8837.677-28.905
606.39906597376-0.979777772101-1.981588809814.084699111170.1553833751385.89129047225-0.145769604519-0.286330705225-0.392256610724-0.06082363719940.4097503038080.7056074669710.373738805944-0.019232391244-0.1641831168760.329286563203-0.0513141967737-0.08681628986980.7798964126730.1938497083080.592303416714-54.8661.707-20.078
616.808043157480.941212941331-2.751155456834.710212862890.9070379211434.96919549576-0.6683801211830.976830265449-0.585211369969-0.5957771551570.0389866619160.6027073087880.496957539206-0.3687538915040.5788506432820.515016149212-0.0733936750485-0.03117629004910.6901561052630.06529819401270.787970258233-51.732-4.587-25.436
625.203574017250.245581727377-0.7277906701551.99979524546-0.2795931691072.64955039979-0.01348645257961.31363082940.26547891739-0.3398826458060.1960552135740.1890529127940.355028076715-1.0283649926-0.2546926688630.4583912088090.00829364809757-0.04630267915650.9924955148710.2539523567210.623767444332-53.5963.694-24.698
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN R AND RESID 332:353 )R332 - 353
2X-RAY DIFFRACTION2( CHAIN R AND RESID 354:442 )R354 - 442
3X-RAY DIFFRACTION3( CHAIN R AND RESID 443:494 )R443 - 494
4X-RAY DIFFRACTION4( CHAIN R AND RESID 495:516 )R495 - 516
5X-RAY DIFFRACTION5( CHAIN H AND RESID 1:17 )H1 - 17
6X-RAY DIFFRACTION6( CHAIN H AND RESID 18:52 )H18 - 52
7X-RAY DIFFRACTION7( CHAIN H AND RESID 53:121 )H53 - 121
8X-RAY DIFFRACTION8( CHAIN H AND RESID 122:185 )H122 - 185
9X-RAY DIFFRACTION9( CHAIN H AND RESID 186:224 )H186 - 224
10X-RAY DIFFRACTION10( CHAIN L AND RESID 1:30 )L1 - 30
11X-RAY DIFFRACTION11( CHAIN L AND RESID 31:76 )L31 - 76
12X-RAY DIFFRACTION12( CHAIN L AND RESID 77:129 )L77 - 129
13X-RAY DIFFRACTION13( CHAIN L AND RESID 130:214 )L130 - 214
14X-RAY DIFFRACTION14( CHAIN A AND RESID 1:17 )A1 - 17
15X-RAY DIFFRACTION15( CHAIN A AND RESID 18:33 )A18 - 33
16X-RAY DIFFRACTION16( CHAIN A AND RESID 34:83 )A34 - 83
17X-RAY DIFFRACTION17( CHAIN A AND RESID 84:133 )A84 - 133
18X-RAY DIFFRACTION18( CHAIN A AND RESID 134:207 )A134 - 207
19X-RAY DIFFRACTION19( CHAIN A AND RESID 208:228 )A208 - 228
20X-RAY DIFFRACTION20( CHAIN B AND RESID 1:18 )B1 - 18
21X-RAY DIFFRACTION21( CHAIN B AND RESID 19:75 )B19 - 75
22X-RAY DIFFRACTION22( CHAIN B AND RESID 76:90 )B76 - 90
23X-RAY DIFFRACTION23( CHAIN B AND RESID 91:113 )B91 - 113
24X-RAY DIFFRACTION24( CHAIN B AND RESID 114:128 )B114 - 128
25X-RAY DIFFRACTION25( CHAIN B AND RESID 129:150 )B129 - 150
26X-RAY DIFFRACTION26( CHAIN B AND RESID 151:163 )B151 - 163
27X-RAY DIFFRACTION27( CHAIN B AND RESID 164:214 )B164 - 214
28X-RAY DIFFRACTION28( CHAIN X AND RESID 333:375 )X333 - 375
29X-RAY DIFFRACTION29( CHAIN X AND RESID 376:442 )X376 - 442
30X-RAY DIFFRACTION30( CHAIN X AND RESID 443:479 )X443 - 479
31X-RAY DIFFRACTION31( CHAIN X AND RESID 480:516 )X480 - 516
32X-RAY DIFFRACTION32( CHAIN C AND RESID 1:39 )C1 - 39
33X-RAY DIFFRACTION33( CHAIN C AND RESID 40:83 )C40 - 83
34X-RAY DIFFRACTION34( CHAIN C AND RESID 84:144 )C84 - 144
35X-RAY DIFFRACTION35( CHAIN C AND RESID 145:224 )C145 - 224
36X-RAY DIFFRACTION36( CHAIN D AND RESID 1:18 )D1 - 18
37X-RAY DIFFRACTION37( CHAIN D AND RESID 19:49 )D19 - 49
38X-RAY DIFFRACTION38( CHAIN D AND RESID 50:76 )D50 - 76
39X-RAY DIFFRACTION39( CHAIN D AND RESID 77:91 )D77 - 91
40X-RAY DIFFRACTION40( CHAIN D AND RESID 92:114 )D92 - 114
41X-RAY DIFFRACTION41( CHAIN D AND RESID 115:129 )D115 - 129
42X-RAY DIFFRACTION42( CHAIN D AND RESID 130:151 )D130 - 151
43X-RAY DIFFRACTION43( CHAIN D AND RESID 152:175 )D152 - 175
44X-RAY DIFFRACTION44( CHAIN D AND RESID 176:198 )D176 - 198
45X-RAY DIFFRACTION45( CHAIN D AND RESID 199:214 )D199 - 214
46X-RAY DIFFRACTION46( CHAIN E AND RESID 1:17 )E1 - 17
47X-RAY DIFFRACTION47( CHAIN E AND RESID 18:33 )E18 - 33
48X-RAY DIFFRACTION48( CHAIN E AND RESID 34:73 )E34 - 73
49X-RAY DIFFRACTION49( CHAIN E AND RESID 74:99 )E74 - 99
50X-RAY DIFFRACTION50( CHAIN E AND RESID 100:123 )E100 - 123
51X-RAY DIFFRACTION51( CHAIN E AND RESID 124:189 )E124 - 189
52X-RAY DIFFRACTION52( CHAIN E AND RESID 190:207 )E190 - 207
53X-RAY DIFFRACTION53( CHAIN E AND RESID 208:217 )E208 - 217
54X-RAY DIFFRACTION54( CHAIN E AND RESID 218:228 )E218 - 228
55X-RAY DIFFRACTION55( CHAIN F AND RESID 1:18 )F1 - 18
56X-RAY DIFFRACTION56( CHAIN F AND RESID 19:75 )F19 - 75
57X-RAY DIFFRACTION57( CHAIN F AND RESID 76:90 )F76 - 90
58X-RAY DIFFRACTION58( CHAIN F AND RESID 91:113 )F91 - 113
59X-RAY DIFFRACTION59( CHAIN F AND RESID 114:128 )F114 - 128
60X-RAY DIFFRACTION60( CHAIN F AND RESID 129:150 )F129 - 150
61X-RAY DIFFRACTION61( CHAIN F AND RESID 151:163 )F151 - 163
62X-RAY DIFFRACTION62( CHAIN F AND RESID 164:214 )F164 - 214

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more