[English] 日本語
Yorodumi
- PDB-5bk2: Crystal structure of maltose binding protein in complex with a pe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bk2
TitleCrystal structure of maltose binding protein in complex with a peristeric synthetic antibody
Components
  • Maltose-binding periplasmic protein
  • sAB Heavy Chain
  • sAB Light Chain
KeywordsSUGAR BINDING PROTEIN / Maltose binding protein / Conformation specific synthetic antibody / Fab fragment
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-maltose / PHOSPHATE ION / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMukherjee, S. / Kossiakoff, A.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Chicago Biomedical Consortium United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Engineered synthetic antibodies as probes to quantify the energetic contributions of ligand binding to conformational changes in proteins.
Authors: Mukherjee, S. / Griffin, D.H. / Horn, J.R. / Rizk, S.S. / Nocula-Lugowska, M. / Malmqvist, M. / Kim, S.S. / Kossiakoff, A.A.
History
DepositionSep 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Maltose-binding periplasmic protein
A: Maltose-binding periplasmic protein
C: sAB Heavy Chain
H: sAB Heavy Chain
D: sAB Light Chain
L: sAB Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,84230
Polymers186,5166
Non-polymers2,32624
Water3,981221
1
B: Maltose-binding periplasmic protein
C: sAB Heavy Chain
D: sAB Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,54116
Polymers93,2583
Non-polymers1,28313
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-77 kcal/mol
Surface area33090 Å2
MethodPISA
2
A: Maltose-binding periplasmic protein
H: sAB Heavy Chain
L: sAB Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,30114
Polymers93,2583
Non-polymers1,04211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8550 Å2
ΔGint-81 kcal/mol
Surface area33290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.170, 42.380, 200.660
Angle α, β, γ (deg.)90.000, 90.070, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain C and (resid 3 through 19 or resid 21...
21(chain H and (resid 3 through 19 or resid 21...
12(chain A and (resid 1 through 41 or resid 43...
22(chain B and (resid 1 through 41 or resid 43...
13(chain D and (resid 1 through 10 or resid 12...
23(chain L and (resid 1 through 10 or resid 12...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERGLYGLY(chain C and (resid 3 through 19 or resid 21...CC3 - 193 - 19
121LEULEUASPASP(chain C and (resid 3 through 19 or resid 21...CC21 - 7621 - 76
131SERSERTYRTYR(chain C and (resid 3 through 19 or resid 21...CC78 - 9878 - 98
141ALAALAGLYGLY(chain C and (resid 3 through 19 or resid 21...CC100 - 155100 - 155
151LEULEUVALVAL(chain C and (resid 3 through 19 or resid 21...CC157 - 168157 - 168
161TRPTRPLEULEU(chain C and (resid 3 through 19 or resid 21...CC170 - 194170 - 194
171SERSERVALVAL(chain C and (resid 3 through 19 or resid 21...CC196 - 214196 - 214
181HISHISPROPRO(chain C and (resid 3 through 19 or resid 21...CC216 - 229216 - 229
211SERSERGLYGLY(chain H and (resid 3 through 19 or resid 21...HD3 - 193 - 19
221LEULEUASPASP(chain H and (resid 3 through 19 or resid 21...HD21 - 7621 - 76
231SERSERTYRTYR(chain H and (resid 3 through 19 or resid 21...HD78 - 9878 - 98
241ALAALASERSER(chain H and (resid 3 through 19 or resid 21...HD100 - 143100 - 143
251THRTHRGLYGLY(chain H and (resid 3 through 19 or resid 21...HD151 - 155151 - 155
261LEULEUVALVAL(chain H and (resid 3 through 19 or resid 21...HD157 - 168157 - 168
271TRPTRPLEULEU(chain H and (resid 3 through 19 or resid 21...HD170 - 194170 - 194
281SERSERVALVAL(chain H and (resid 3 through 19 or resid 21...HD196 - 214196 - 214
291HISHISPROPRO(chain H and (resid 3 through 19 or resid 21...HD216 - 229216 - 229
112LYSLYSASPASP(chain A and (resid 1 through 41 or resid 43...AB1 - 4132 - 72
122LEULEUASPASP(chain A and (resid 1 through 41 or resid 43...AB43 - 13674 - 167
132GLUGLUPHEPHE(chain A and (resid 1 through 41 or resid 43...AB138 - 169169 - 200
142TYRTYRGLYGLY(chain A and (resid 1 through 41 or resid 43...AB171 - 174202 - 205
152LYSLYSLYSLYS(chain A and (resid 1 through 41 or resid 43...AB175206
162LYSLYSASNASN(chain A and (resid 1 through 41 or resid 43...AB1 - 36732 - 398
172LYSLYSASNASN(chain A and (resid 1 through 41 or resid 43...AB1 - 36732 - 398
182LYSLYSASNASN(chain A and (resid 1 through 41 or resid 43...AB1 - 36732 - 398
192LYSLYSASNASN(chain A and (resid 1 through 41 or resid 43...AB1 - 36732 - 398
212LYSLYSASPASP(chain B and (resid 1 through 41 or resid 43...BA1 - 4132 - 72
222LEULEUASPASP(chain B and (resid 1 through 41 or resid 43...BA43 - 13674 - 167
232GLUGLUPHEPHE(chain B and (resid 1 through 41 or resid 43...BA138 - 169169 - 200
242TYRTYRALAALA(chain B and (resid 1 through 41 or resid 43...BA171 - 312202 - 343
252ASPASPLEULEU(chain B and (resid 1 through 41 or resid 43...BA314 - 361345 - 392
262LYSLYSLYSLYS(chain B and (resid 1 through 41 or resid 43...BA362393
272LYSLYSASNASN(chain B and (resid 1 through 41 or resid 43...BA1 - 36732 - 398
282LYSLYSASNASN(chain B and (resid 1 through 41 or resid 43...BA1 - 36732 - 398
292LYSLYSASNASN(chain B and (resid 1 through 41 or resid 43...BA1 - 36732 - 398
2102LYSLYSASNASN(chain B and (resid 1 through 41 or resid 43...BA1 - 36732 - 398
2112LYSLYSASNASN(chain B and (resid 1 through 41 or resid 43...BA1 - 36732 - 398
2122LYSLYSASNASN(chain B and (resid 1 through 41 or resid 43...BA1 - 36732 - 398
113SERSERSERSER(chain D and (resid 1 through 10 or resid 12...DE1 - 101 - 10
123LEULEULEULEU(chain D and (resid 1 through 10 or resid 12...DE1212
133ALAALAGLYGLY(chain D and (resid 1 through 10 or resid 12...DE14 - 6514 - 65
143ARGARGGLNGLN(chain D and (resid 1 through 10 or resid 12...DE67 - 15767 - 157
153GLYGLYTHRTHR(chain D and (resid 1 through 10 or resid 12...DE159 - 166159 - 166
163GLNGLNALAALA(chain D and (resid 1 through 10 or resid 12...DE168 - 195168 - 195
173GLUGLUSERSER(chain D and (resid 1 through 10 or resid 12...DE197 - 204197 - 204
183PROPROCYSCYS(chain D and (resid 1 through 10 or resid 12...DE206 - 216206 - 216
213SERSERSERSER(chain L and (resid 1 through 10 or resid 12...LF1 - 101 - 10
223LEULEULEULEU(chain L and (resid 1 through 10 or resid 12...LF1212
233ALAALAGLYGLY(chain L and (resid 1 through 10 or resid 12...LF14 - 6514 - 65
243ARGARGGLNGLN(chain L and (resid 1 through 10 or resid 12...LF67 - 15767 - 157
253GLYGLYTHRTHR(chain L and (resid 1 through 10 or resid 12...LF159 - 166159 - 166
263GLNGLNALAALA(chain L and (resid 1 through 10 or resid 12...LF168 - 195168 - 195
273GLUGLUSERSER(chain L and (resid 1 through 10 or resid 12...LF197 - 204197 - 204
283PROPROCYSCYS(chain L and (resid 1 through 10 or resid 12...LF206 - 216206 - 216

NCS ensembles :
ID
1
2
3

-
Components

-
Antibody , 2 types, 4 molecules CHDL

#2: Antibody sAB Heavy Chain


Mass: 25478.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRH2.2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#3: Antibody sAB Light Chain


Mass: 23604.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRH2.2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21

-
Protein / Sugars , 2 types, 4 molecules BA

#1: Protein Maltose-binding periplasmic protein / MBP / MMBP / Maltodextrin-binding protein


Mass: 44175.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: malE, b4034, JW3994 / Plasmid: pHFT2 / Details (production host): N-terminal 10xHis, Flag, TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AEX9
#4: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 243 molecules

#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M KSCN and 18% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.6→19.938 Å / Num. obs: 57286 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.514 % / Biso Wilson estimate: 44.42 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.2 / Rrim(I) all: 0.218 / Χ2: 0.944 / Net I/σ(I): 8.41
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.76.9561.381.7460820.6311.49100
2.7-2.86.8891.0772.1952530.7131.165100
2.8-2.96.8290.8352.8545340.8020.90499.9
2.9-36.5850.6463.4539880.8520.70199.8
3-46.5090.2846.94214260.9710.30999.6
4-55.5160.08515.675920.9920.09598
5-66.9450.08618.0935000.9960.09399.8
6-106.5630.07319.7538010.9970.07999.8
10-156.5670.05626.167670.9980.06199.4
15-205.7680.06621.881980.9960.07298.5
19.938-204.80.0522.321450.9970.05589

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
MD2data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PGF

3pgf


Resolution: 2.6→19.938 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.45
RfactorNum. reflection% reflection
Rfree0.2588 2864 5.01 %
Rwork0.2121 --
obs0.2144 57135 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 159.3 Å2 / Biso mean: 53.9958 Å2 / Biso min: 18.61 Å2
Refinement stepCycle: final / Resolution: 2.6→19.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12388 0 139 223 12750
Biso mean--56.7 43.22 -
Num. residues----1614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312957
X-RAY DIFFRACTIONf_angle_d0.54317659
X-RAY DIFFRACTIONf_chiral_restr0.0431947
X-RAY DIFFRACTIONf_plane_restr0.0042238
X-RAY DIFFRACTIONf_dihedral_angle_d12.6087758
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11C1857X-RAY DIFFRACTION7.695TORSIONAL
12H1857X-RAY DIFFRACTION7.695TORSIONAL
21A3358X-RAY DIFFRACTION7.695TORSIONAL
22B3358X-RAY DIFFRACTION7.695TORSIONAL
31D1910X-RAY DIFFRACTION7.695TORSIONAL
32L1910X-RAY DIFFRACTION7.695TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.64480.33871990.293726692868100
2.6448-2.69270.32651790.293626352814100
2.6927-2.74440.33981390.276126482787100
2.7444-2.80030.33171130.275327592872100
2.8003-2.8610.31281440.266927182862100
2.861-2.92730.27451260.254426872813100
2.9273-3.00030.28851390.240427072846100
3.0003-3.08110.27981700.251826522822100
3.0811-3.17150.24121510.227126802831100
3.1715-3.27340.28181150.214527662881100
3.2734-3.38990.26711360.21326742810100
3.3899-3.52490.25261250.191127742899100
3.5249-3.68430.27181040.189327232827100
3.6843-3.87720.27131370.19382736287399
3.8772-4.11820.23991620.1932606276898
4.1182-4.43290.21991250.18722676280198
4.4329-4.87310.23571540.18642709286398
4.8731-5.56480.22141420.204927602902100
5.5648-6.96110.28331760.22828012977100
6.9611-19.93890.21021280.186428913019100
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)
16.5692.26692.85192.61271.91872.2858-0.29411.1356-1.2065-0.63580.04960.17560.9691-1.0022-0.060.6907-0.3245-0.08260.9671-0.19070.7266-44.685-0.56161.567
22.4532-0.1678-0.56880.78930.15443.3956-0.06750.32110.0851-0.05420.10210.23270.0808-0.6725-0.0330.2916-0.0192-0.03620.4190.01630.4673-39.30914.33678.208
36.9455-2.0192.16133.96640.22855.38630.2711-0.06370.7439-0.0724-0.38220.4351-1.4173-1.30440.2730.81390.16950.19530.5261-0.0060.6719-37.43330.08823.191
44.9754-0.78610.76141.37150.90664.66910.0934-0.19330.51660.2748-0.01460.41560.0806-1.0198-0.06840.5077-0.02910.1030.45130.0140.3954-32.8514.58228.179
53.16650.4499-0.93251.25930.24884.4053-0.20350.9194-0.2035-0.26110.25720.199-0.1012-0.5033-0.110.456-0.11810.03230.6288-0.05860.4172-26.63411.578-3.837
62.70130.26910.11590.8549-0.17634.4764-0.07350.4115-0.3220.05460.2671-0.06120.31410.307-0.16190.5044-0.07590.03910.3601-0.09160.4182-18.2966.7448.152
73.4559-0.1134-0.52171.74980.77615.1165-0.0260.61270.0595-0.11110.06170.1978-0.0555-0.7841-0.10170.3683-0.06590.03070.50910.06950.3466-31.29214.3556.134
83.20810.0553-0.13851.81240.76914.9192-0.04020.17940.10020.0171-0.00940.39850.067-1.33840.10450.4184-0.05340.08520.73090.0760.5028-41.73414.48316.066
95.4139-0.8968-2.33080.62852.22567.89-0.07440.1803-0.0220.11540.5271-0.3760.260.7663-0.34970.459-0.017-0.00930.4574-0.11780.4335-10.719.65514.229
103.4308-0.2102-5.34841.8-0.66768.8672-0.1692-0.1054-0.41060.1788-0.0024-0.10820.08030.40330.62170.27490.0721-0.02610.55620.09150.442229.688-20.20580.855
114.3131-1.0147-5.77891.12551.09157.83070.36870.0499-0.2753-0.1249-0.39460.0948-0.52390.25570.03190.35680.0287-0.06150.31560.06250.375722.453-13.39688.637
129.48283.64693.0993.51121.19074.59920.1203-1.20860.69790.6637-0.577-0.4322-0.67350.12840.46040.6049-0.136-0.08730.36210.01650.508729.633-7.37786.233
137.045-0.1053-2.45740.4758-0.83654.5942-0.2747-0.50110.14840.08770.0781-0.226-0.14460.69140.190.3287-0.0435-0.03110.3067-0.01570.419124.815-14.60187.744
146.19442.5549-6.2322.9237-1.10287.4563-0.8891-1.1115-1.4333-0.13330.4658-0.06990.53741.07511.06280.4330.1891-0.0620.66260.12750.490735.752-21.589.103
155.07230.567-0.48482.9583-0.30464.32310.3326-0.10570.3161-0.0030.6114-0.0631-1.0421.3320.28590.5746-0.34520.06731.0021-0.00630.509240.09238.437.879
166.12491.12351.29581.65040.81366.2432-0.34630.45850.4364-0.3768-0.30880.152-0.14341.06960.06620.6551-0.01240.06450.72630.00550.412733.33133.60927.308
174.82330.8368-1.66722.5861-0.98641.768-0.5009-0.1754-0.9967-0.4984-0.7504-1.1898-0.11891.25180.32110.53280.00840.12971.01110.08110.649344.90125.64531.349
182.86530.4964-0.74092.5384-0.92873.6977-0.01470.8007-0.4536-0.26010.0822-0.6584-0.20131.41060.1970.4525-0.14230.07790.8585-0.03450.339737.09632.40229.986
192.6545-1.3532-1.03043.264-3.13095.61690.0961-0.45870.02660.6428-0.3014-0.983-1.12781.66710.52460.5769-0.4280.08561.67370.18340.881449.34238.74333.429
207.71611.8971-2.17291.9896-1.35833.4134-0.05080.0223-1.0512-0.2896-0.1279-0.49180.1134-0.06280.10730.46030.03630.0290.1613-0.02620.37272.302-5.36259.082
214.0903-1.5279-1.00764.13710.32061.3312-0.01540.4551-0.1858-0.1219-0.0010.14390.268-0.14020.01070.2935-0.008-0.01620.1589-0.01070.2995-7.231-2.09560.064
224.99712.75060.29174.86060.97176.37790.04780.16370.40150.1179-0.2349-0.64910.21710.95490.15510.20370.022-0.00490.2507-0.0190.2536-0.7113.41168.678
232.6974-0.5420.52911.53730.90651.267-0.06730.03270.116-0.19340.002-0.0371-0.1571-0.07750.06480.4295-0.00010.00310.20970.03220.3207-2.4484.08959.518
243.8514-2.25080.14091.5704-0.36060.1889-0.09090.1106-0.15070.1939-0.01120.05280.0804-0.02130.09530.4258-0.0279-0.07250.2116-0.03290.3191-1.506-2.20866.637
256.32810.2896-1.54353.98822.29693.15930.2905-1.0221-0.6660.6478-0.4867-0.39130.57791.24170.16710.4098-0.018-0.1330.37690.06280.375524.466-23.47580.33
262.4706-1.47230.77251.12470.56765.95280.013-0.0540.1885-0.08290.05160.4286-0.0702-0.0025-0.06770.31430.02580.00320.16580.04960.265716.662-17.06972.718
273.45160.7396-0.76134.7691-6.39388.80110.3869-0.3332-0.44140.33550.1357-0.19840.4121-0.0347-0.33340.4396-0.0678-0.1160.29070.12970.399219.812-24.93779.605
285.6384-0.2594-0.15668.3444-3.61082.4304-0.02180.25-0.45260.4546-0.2676-0.2416-0.35910.16330.20570.40260.0247-0.01940.1712-0.00070.32718.425-25.90968.66
295.1512-0.73752.23265.8752-3.9085.21870.0346-0.30870.0376-0.1678-0.132-1.3390.826-0.2111-0.0550.38830.0147-0.08050.292-0.02420.500924.534-26.92368.722
305.20390.0322.66081.58383.13727.5126-0.20010.85541.4509-0.5846-0.6222-0.2918-0.8458-0.33950.35140.65860.01160.1340.32890.12370.5658-3.17535.68838.936
318.0903-1.32964.33392.1253-0.67755.00640.3615-0.4674-0.0155-0.163-0.1380.04220.1376-0.502-0.13620.43680.04310.04050.148-0.01680.2413-0.51626.50946.53
324.6016-0.5641.58184.11440.23255.0348-0.00570.966-0.8775-0.28150.061-0.7361-0.36430.7369-0.02620.3991-0.0122-0.01140.365-0.05170.38995.37322.21636.882
334.58690.92230.54141.1073-0.07412.60410.15490.108-0.50160.1053-0.0672-0.17360.0416-0.05040.05280.5410.03070.0070.1454-0.03880.411-4.16119.09743.83
344.14590.98682.14991.14320.48883.19260.53460.5539-0.3813-0.4441-0.25830.1330.53670.2953-0.20930.5899-0.0404-0.04270.3204-0.01890.28285.54921.07542.025
352.04080.73791.38010.35710.82981.95430.15870.1327-0.3089-0.2288-0.1018-0.26020.0780.432-0.0520.60620.02310.03010.27880.01210.4285-14.33217.83929.627
363.63640.35453.70291.3040.86574.7078-0.02710.13040.00170.0327-0.12940.4612-0.44970.01040.23070.4872-0.00780.01260.24220.05690.32323.32527.51737.298
372.7151-0.53781.37162.20681.49853.73730.0657-0.01750.28540.15380.0355-0.1069-0.26841.2734-0.1470.2709-0.0454-0.04090.4357-0.04140.376630.43534.98546.894
385.11072.7313-0.63372.768-2.03395.3048-0.01990.73780.2775-0.3020.3267-0.0956-0.3746-0.1635-0.23250.4674-0.07050.01420.37020.01370.382928.19736.44141.948
393.49280.43090.34983.0909-1.99024.9554-0.04590.47580.3711-0.61530.25920.1609-0.49380.1986-0.21580.6003-0.11810.03550.34970.10560.349926.55938.87437.649
402.04940.85140.34722.4341-1.46691.3031-0.28630.24170.9831-0.15920.38310.0347-1.55240.54390.01081.1884-0.5069-0.0251.20250.31761.298434.85856.36433.666
412.95671.3483-0.73393.2528-3.54084.24760.10720.55650.7199-0.34420.1430.1473-1.79880.0813-0.29160.7635-0.12940.09560.34160.03820.391726.43644.42846.521
424.05960.06560.20155.6195-2.36355.2858-0.3801-0.66260.4808-0.09290.2916-0.92510.25240.4465-0.00440.36640.0942-0.04280.4649-0.11520.2763-3.142-0.02388.309
433.8576-0.1091-0.07851.3977-1.9953.1399-0.1371-0.29230.00280.40210.21360.0345-0.0868-0.0189-0.10620.33230.0124-0.00760.2056-0.03560.2761-11.333-0.84982.924
441.89252.7148-0.75717.3302-5.28165.4048-0.0189-0.4295-0.2833-0.0656-0.00630.19790.3670.27760.03480.33750.15440.04320.38660.020.3592-6.494-7.68584.494
453.3526-0.3071-0.07010.8482-1.35412.1503-0.3510.09610.39340.30920.1470.2076-0.43750.09180.24730.3299-0.013-0.09290.2203-0.05160.3841-7.4058.85176.144
462.35890.58331.44023.4814-3.42155.19980.7758-0.10610.1261-0.8794-0.6156-0.07930.26090.4901-0.18650.3970.1171-0.00790.2972-0.01690.33023.734-13.59193.71
472.00671.9254-0.17529.44742.16343.6740.0218-0.5351-0.92890.5775-0.4306-0.26-0.13570.2829-0.11840.54720.1337-0.11030.8298-0.18470.45256.44610.72524.787
484.14672.9218-0.75316.4317-0.50710.1764-0.06361.4114-0.3256-0.2770.3791-0.253-0.07790.0086-0.26730.7001-0.02780.02760.7753-0.07780.305811.91323.93313.619
494.0443-0.6788-1.23121.6636-0.07885.1325-0.36120.918-0.6267-0.52120.5352-0.2755-0.25080.32940.1150.5282-0.01770.00150.3915-0.11070.37340.6517.77822.35
502.880.5075-1.19561.9215-0.64581.13680.0680.23760.41270.47480.4382-0.2156-0.53380.68560.0380.4745-0.091-0.04280.6196-0.14450.18684.88930.63326.659
514.74251.6824-1.11551.337-0.92414.06970.34170.99390.393-0.1542-0.30850.0798-0.0526-0.4074-0.16980.57520.0361-0.05650.5352-0.00160.386-4.06329.26117.817
527.60960.1528-1.22710.41431.09263.1861-0.45011.3095-1.23020.01090.3805-0.1931-0.21620.2040.08070.6206-0.08310.04670.7197-0.19620.26591.98120.01312.938
534.34831.798-2.5473.2132-0.23855.55060.24071.21540.4691-0.10110.1302-0.3224-1.0780.6685-0.25210.9335-0.1884-0.01320.9003-0.02410.50269.57735.0315.168
542.7679-1.2433-0.87541.6142-1.0742.33110.13510.2363-0.7112-0.11470.21280.3687-0.07081.00390.07950.5375-0.1624-0.04920.5039-0.16540.30275.34621.53524.372
556.67280.7556-1.35081.18950.12195.4878-0.5319-0.1239-0.5143-0.47140.4235-0.15590.91080.18670.16280.51330.05390.00570.294-0.08190.47860.54513.88527.409
563.6390.4473-1.35081.526-0.31640.5168-0.59451.2805-0.4405-0.5247-0.05780.2351-0.7788-0.4695-0.01660.7266-0.30580.01920.88730.06810.268921.19733.14515.402
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 1:42 )B1 - 42
2X-RAY DIFFRACTION2( CHAIN B AND RESID 43:367 )B43 - 367
3X-RAY DIFFRACTION3( CHAIN A AND RESID 1:42 )A1 - 42
4X-RAY DIFFRACTION4( CHAIN A AND RESID 43:105 )A43 - 105
5X-RAY DIFFRACTION5( CHAIN A AND RESID 106:153 )A106 - 153
6X-RAY DIFFRACTION6( CHAIN A AND RESID 154:218 )A154 - 218
7X-RAY DIFFRACTION7( CHAIN A AND RESID 219:272 )A219 - 272
8X-RAY DIFFRACTION8( CHAIN A AND RESID 273:333 )A273 - 333
9X-RAY DIFFRACTION9( CHAIN A AND RESID 334:367 )A334 - 367
10X-RAY DIFFRACTION10( CHAIN D AND RESID 113:130 )D113 - 130
11X-RAY DIFFRACTION11( CHAIN D AND RESID 131:152 )D131 - 152
12X-RAY DIFFRACTION12( CHAIN D AND RESID 153:165 )D153 - 165
13X-RAY DIFFRACTION13( CHAIN D AND RESID 166:206 )D166 - 206
14X-RAY DIFFRACTION14( CHAIN D AND RESID 207:216 )D207 - 216
15X-RAY DIFFRACTION15( CHAIN L AND RESID 113:130 )L113 - 130
16X-RAY DIFFRACTION16( CHAIN L AND RESID 131:146 )L131 - 146
17X-RAY DIFFRACTION17( CHAIN L AND RESID 147:160 )L147 - 160
18X-RAY DIFFRACTION18( CHAIN L AND RESID 161:206 )L161 - 206
19X-RAY DIFFRACTION19( CHAIN L AND RESID 207:216 )L207 - 216
20X-RAY DIFFRACTION20( CHAIN C AND RESID 3:20 )C3 - 20
21X-RAY DIFFRACTION21( CHAIN C AND RESID 21:42 )C21 - 42
22X-RAY DIFFRACTION22( CHAIN C AND RESID 43:55 )C43 - 55
23X-RAY DIFFRACTION23( CHAIN C AND RESID 56:102 )C56 - 102
24X-RAY DIFFRACTION24( CHAIN C AND RESID 103:140 )C103 - 140
25X-RAY DIFFRACTION25( CHAIN C AND RESID 141:161 )C141 - 161
26X-RAY DIFFRACTION26( CHAIN C AND RESID 162:191 )C162 - 191
27X-RAY DIFFRACTION27( CHAIN C AND RESID 192:205 )C192 - 205
28X-RAY DIFFRACTION28( CHAIN C AND RESID 206:219 )C206 - 219
29X-RAY DIFFRACTION29( CHAIN C AND RESID 220:230 )C220 - 230
30X-RAY DIFFRACTION30( CHAIN H AND RESID 3:10 )H3 - 10
31X-RAY DIFFRACTION31( CHAIN H AND RESID 11:35 )H11 - 35
32X-RAY DIFFRACTION32( CHAIN H AND RESID 36:47 )H36 - 47
33X-RAY DIFFRACTION33( CHAIN H AND RESID 48:86 )H48 - 86
34X-RAY DIFFRACTION34( CHAIN H AND RESID 87:102 )H87 - 102
35X-RAY DIFFRACTION35( CHAIN H AND RESID 103:113 )H103 - 113
36X-RAY DIFFRACTION36( CHAIN H AND RESID 114:127 )H114 - 127
37X-RAY DIFFRACTION37( CHAIN H AND RESID 128:143 )H128 - 143
38X-RAY DIFFRACTION38( CHAIN H AND RESID 151:166 )H151 - 166
39X-RAY DIFFRACTION39( CHAIN H AND RESID 167:200 )H167 - 200
40X-RAY DIFFRACTION40( CHAIN H AND RESID 201:209 )H201 - 209
41X-RAY DIFFRACTION41( CHAIN H AND RESID 210:229 )H210 - 229
42X-RAY DIFFRACTION42( CHAIN D AND RESID 1:19 )D1 - 19
43X-RAY DIFFRACTION43( CHAIN D AND RESID 20:76 )D20 - 76
44X-RAY DIFFRACTION44( CHAIN D AND RESID 77:91 )D77 - 91
45X-RAY DIFFRACTION45( CHAIN D AND RESID 92:104 )D92 - 104
46X-RAY DIFFRACTION46( CHAIN D AND RESID 105:112 )D105 - 112
47X-RAY DIFFRACTION47( CHAIN L AND RESID 1:8 )L1 - 8
48X-RAY DIFFRACTION48( CHAIN L AND RESID 9:26 )L9 - 26
49X-RAY DIFFRACTION49( CHAIN L AND RESID 27:39 )L27 - 39
50X-RAY DIFFRACTION50( CHAIN L AND RESID 40:49 )L40 - 49
51X-RAY DIFFRACTION51( CHAIN L AND RESID 50:62 )L50 - 62
52X-RAY DIFFRACTION52( CHAIN L AND RESID 63:76 )L63 - 76
53X-RAY DIFFRACTION53( CHAIN L AND RESID 77:85 )L77 - 85
54X-RAY DIFFRACTION54( CHAIN L AND RESID 86:91 )L86 - 91
55X-RAY DIFFRACTION55( CHAIN L AND RESID 92:104 )L92 - 104
56X-RAY DIFFRACTION56( CHAIN L AND RESID 105:112 )L105 - 112

+
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