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- PDB-6bf4: Crystal Structure of HIV-1 Clade AE Strain CNE55 gp120 Core in Co... -

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Basic information

Entry
Database: PDB / ID: 6bf4
TitleCrystal Structure of HIV-1 Clade AE Strain CNE55 gp120 Core in Complex with Neutralizing Antibody VRC-PG05 that Targets the Center of the Silent Face on the Outer Domain of gp120
Components
  • (VRC-PG05 Fab ...) x 2
  • HIV-1 clade AE gp120 core
Keywordsviral protein/immune system / Antibody / HIV-1 / Silent face / glycan / gp120 / viral protein-IMMUNE SYSTEM complex
Function / homology
Function and homology information


: / positive regulation of establishment of T cell polarity / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / apoptotic process ...: / positive regulation of establishment of T cell polarity / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / apoptotic process / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.382 Å
AuthorsZhou, T. / Kwong, P.D.
CitationJournal: Immunity / Year: 2018
Title: A Neutralizing Antibody Recognizing Primarily N-Linked Glycan Targets the Silent Face of the HIV Envelope.
Authors: Zhou, T. / Zheng, A. / Baxa, U. / Chuang, G.Y. / Georgiev, I.S. / Kong, R. / O'Dell, S. / Shahzad-Ul-Hussan, S. / Shen, C.H. / Tsybovsky, Y. / Bailer, R.T. / Gift, S.K. / Louder, M.K. / ...Authors: Zhou, T. / Zheng, A. / Baxa, U. / Chuang, G.Y. / Georgiev, I.S. / Kong, R. / O'Dell, S. / Shahzad-Ul-Hussan, S. / Shen, C.H. / Tsybovsky, Y. / Bailer, R.T. / Gift, S.K. / Louder, M.K. / McKee, K. / Rawi, R. / Stevenson, C.H. / Stewart-Jones, G.B.E. / Taft, J.D. / Waltari, E. / Yang, Y. / Zhang, B. / Shivatare, S.S. / Shivatare, V.S. / Lee, C.D. / Wu, C.Y. / Mullikin, J.C. / Bewley, C.A. / Burton, D.R. / Polonis, V.R. / Shapiro, L. / Wong, C.H. / Mascola, J.R. / Kwong, P.D. / Wu, X.
History
DepositionOct 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.journal_abbrev ..._chem_comp.name / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / 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.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 clade AE gp120 core
B: VRC-PG05 Fab heavy chain
C: VRC-PG05 Fab light chain
G: HIV-1 clade AE gp120 core
H: VRC-PG05 Fab heavy chain
L: VRC-PG05 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,01236
Polymers174,3786
Non-polymers13,63330
Water3,171176
1
A: HIV-1 clade AE gp120 core
B: VRC-PG05 Fab heavy chain
C: VRC-PG05 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,76118
Polymers87,1893
Non-polymers6,57215
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: HIV-1 clade AE gp120 core
H: VRC-PG05 Fab heavy chain
L: VRC-PG05 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,25118
Polymers87,1893
Non-polymers7,06115
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)231.438, 89.255, 123.407
Angle α, β, γ (deg.)90.000, 119.150, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AG

#1: Protein HIV-1 clade AE gp120 core


Mass: 38218.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Synthesized / Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: CNE55 / Plasmid: PVRC8400 / Details (production host): CMV-based vector / Cell line (production host): GNTI- / Production host: Homo sapiens (human) / References: UniProt: D7S2G1*PLUS

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Antibody , 2 types, 4 molecules BHCL

#2: Antibody VRC-PG05 Fab heavy chain


Mass: 24636.877 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Details (production host): CMV-based vector / Cell line (production host): GNTI- / Production host: Homo sapiens (human)
#3: Antibody VRC-PG05 Fab light chain


Mass: 24334.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): GNTI- / Production host: Homo sapiens (human)

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Sugars , 8 types, 22 molecules

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


Type: oligosaccharide / Mass: 1721.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6[DManpa1-2DManpa1-3]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-i1_g2-h1_i2-j1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1559.386 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1883.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,11,10/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2-2-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-j1_h2-i1_j2-k1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#9: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#10: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#11: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 184 molecules

#12: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#13: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 9.8% PEG 4000, 0.196 M Sodium acetate, 98 mM Tris/Cl-, pH 8.5 and 0.6% 1,6-hexanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 77984 / % possible obs: 88.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 49.59 Å2 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.058 / Rrim(I) all: 0.109 / Χ2: 1.647 / Net I/σ(I): 10.6 / Num. measured all: 260022
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.38-2.422.10.44722070.7030.3460.5690.94550.4
2.42-2.472.20.44825740.6840.3370.5641.10159.2
2.47-2.512.40.40828890.7540.2970.5071.07466.4
2.51-2.562.50.41431520.7760.2910.5081.11372
2.56-2.622.70.40333770.8130.2750.491.20877.1
2.62-2.682.90.39836010.8430.2640.481.17882.6
2.68-2.753.10.35638650.8850.2290.4251.26888.2
2.75-2.823.20.31441820.9130.1980.3721.32195.3
2.82-2.93.50.28842540.9350.1790.341.38798.2
2.9-33.70.24443620.9550.1480.2861.44699
3-3.113.80.20543480.9670.1240.241.64399.1
3.11-3.233.80.16643470.9750.1010.1951.85799.1
3.23-3.383.70.13543110.9820.0830.1591.92699
3.38-3.553.70.11743640.9840.0720.1382.1498.8
3.55-3.783.70.09943290.9880.0610.1172.21798.8
3.78-4.073.60.08443430.990.0520.0992.04298.6
4.07-4.483.60.07243510.9890.0460.0861.91798.5
4.48-5.133.60.06643430.9910.0410.0781.8198.3
5.13-6.463.60.06343900.9920.0390.0741.62598.4
6.46-503.50.05843950.9940.0360.0681.46897.1

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Processing

Software
NameVersionClassification
SERGUIdata collection
SCALEPACKdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YDL

4ydl


Resolution: 2.382→39.847 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.1
RfactorNum. reflection% reflection
Rfree0.2284 3886 4.99 %
Rwork0.1922 --
obs0.194 77824 88.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 221.93 Å2 / Biso mean: 90.1428 Å2 / Biso min: 20.31 Å2
Refinement stepCycle: final / Resolution: 2.382→39.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12045 0 903 176 13124
Biso mean--87.3 54.67 -
Num. residues----1553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313310
X-RAY DIFFRACTIONf_angle_d0.67818202
X-RAY DIFFRACTIONf_chiral_restr0.0472217
X-RAY DIFFRACTIONf_plane_restr0.0042215
X-RAY DIFFRACTIONf_dihedral_angle_d14.8018013
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3825-2.41150.2753800.2611404148447
2.4115-2.4420.2948870.25471651173856
2.442-2.47420.2966740.25361818189261
2.4742-2.5080.30831060.25081952205867
2.508-2.54390.28521160.26232088220470
2.5439-2.58180.28841140.26922209232374
2.5818-2.62220.3181070.26652290239777
2.6222-2.66520.37011090.29122408251781
2.6652-2.71110.32321240.27962516264084
2.7111-2.76040.29291220.2582720284290
2.7604-2.81350.29841670.23752796296395
2.8135-2.87090.30161550.23832908306398
2.8709-2.93330.2911480.24242924307299
2.9333-3.00150.24981560.23592929308599
3.0015-3.07650.28361520.24872959311199
3.0765-3.15970.26341460.23212976312299
3.1597-3.25260.2591730.22412913308699
3.2526-3.35760.25661460.20092944309099
3.3576-3.47750.22171650.20192938310399
3.4775-3.61660.2071670.19952961312899
3.6166-3.78110.24791650.19222909307499
3.7811-3.98030.20281600.18122958311899
3.9803-4.22940.19991530.17032956310999
4.2294-4.55550.19271550.14932934308998
4.5555-5.01320.19351500.14612963311398
5.0132-5.73680.17251480.15712950309898
5.7368-7.22070.22721700.18942986315698
7.2207-39.85270.1931710.15622978314997
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)
12.25361.99471.41493.844-0.64151.9633-0.0022-0.5120.75220.57010.120.9065-1.0658-0.8737-0.12041.4590.68420.37141.56190.05881.0454-44.58869.9091.692
22.04181.85370.25492.43160.44960.1102-0.3187-0.5791.3461.75220.54931.1044-1.3713-0.4145-0.25322.13350.68150.25161.27970.14271.1216-34.98679.029-1.913
32.68820.98310.33523.56180.10514.17260.1762-0.34510.03850.9164-0.0025-0.0998-0.64120.202-0.17561.12380.36870.05431.13110.09980.4364-26.9358.812-0.799
45.14243.4061-3.74525.3228-1.61334.0988-0.2972-0.0319-0.5877-1.3012-0.03960.39890.666-0.55910.36740.43460.1517-0.2270.69810.07360.7915-49.70860.316-49.715
54.1187-1.45961.40613.1982-0.43963.8663-0.1439-0.5203-0.40720.14210.26740.762-0.2726-0.5245-0.12050.48450.2490.00210.56280.13450.5888-44.49362.401-39.063
62.942-1.5367-1.08272.45890.79622.19220.25990.8474-1.8848-0.6978-0.64491.7782-0.0606-0.48570.26590.8240.2879-0.55830.817-0.37321.5835-44.39745.402-67.142
70.25661.06950.39786.4082-0.79823.52990.39220.9633-1.83490.52120.24560.77940.2064-1.1682-0.50010.78550.2284-0.4661.1854-0.37342.2697-52.71945.254-66.3
82.88351.33041.01031.16512.14676.5502-0.0832-0.2501-0.3612-0.0894-0.02260.026-0.61410.0040.11540.33790.06680.01540.23340.090.3476-20.27753.346-43.356
95.04220.9265-2.48689.2608-6.18244.8272-0.3796-1.1514-0.39250.44790.3389-0.1905-0.47110.39940.13380.66010.34040.02810.68430.09670.3889-25.01460.261-24.68
108.1429-2.15740.47123.37320.38862.0418-0.01310.3334-0.6388-0.07910.2070.67710.0039-0.6481-0.24410.41160.0605-0.03270.28490.1080.5133-33.04649.825-42.182
119.15410.70011.26018.88816.78247.7512-0.7128-0.6096-1.87041.40350.39630.41170.9459-0.0060.13030.530.20560.12220.52010.3190.7136-29.65145.05-32.354
123.3969-2.05980.43752.98550.22893.26520.15640.4214-0.8724-0.4058-0.11490.76340.1172-0.1649-0.150.38090.0331-0.13040.3171-0.06390.6026-30.45448.427-53.941
135.3088-0.83674.97351.21720.21386.02190.33250.984-0.8544-1.1651-0.7320.4477-0.70810.0270.12431.10930.3397-0.38850.6828-0.30130.8085-28.67645.932-70.455
141.0090.586-0.04920.43-0.60122.6238-0.03671.5556-0.1292-0.97010.00230.5074-0.6484-0.60980.12391.79920.7481-0.9221.5962-0.67920.6379-35.66747.309-83.029
157.1585-1.23365.50210.5777-1.09364.25210.99741.2007-1.195-0.8906-1.07491.03650.6127-0.8406-0.09871.30050.4125-0.32931.5118-0.77991.2328-31.14837.642-81.196
164.3669-3.01-2.24394.89545.04474.97450.2077-0.1433-0.9081.1066-0.61530.67621.3343-0.83130.32330.7555-0.1785-0.00951.01390.06830.5634-33.18416.69832.505
172.6045-1.72830.27636.78781.45866.02-0.02370.3525-1.0850.01250.1493-0.08221.2665-0.3507-0.1440.6412-0.2458-0.00830.7632-0.16710.7647-26.90213.79330.726
189.8646-7.28082.6535.4132-1.75088.59980.0610.4615-1.5229-0.56660.15592.24880.7243-1.1595-0.13580.5211-0.2353-0.03391.1678-0.0590.6657-36.27323.60623.803
198.2761-1.55555.78959.1618-2.12447.8753-0.46260.369-0.8838-1.11460.35720.9417-0.1626-1.39320.13570.7436-0.262-0.23871.64660.31060.9352-45.76938.0216.693
202.6326-1.22091.05647.00330.9984.0061-0.1310.6294-0.59470.12970.4363-0.3860.5763-0.5525-0.28970.409-0.19920.11651.0535-0.13330.599-27.94420.21828.406
212.5643-2.5161-4.74754.11494.20378.88260.00480.2949-1.21780.66150.0497-0.13851.99011.44380.01321.21410.2767-0.13370.878-0.33061.3802-17.4125.66724.549
227.3733-1.67973.55027.79952.81757.52420.20631.0314-1.17321.05950.0075-0.05560.48890.7252-0.21560.37630.050.03720.8129-0.20350.5447-26.17721.21730.116
233.61162.2134-2.60981.96040.34197.8023-0.51191.012-1.1032-0.5940.7193-0.46070.8742-0.0304-0.12550.505-0.10150.14921.2823-0.38860.5853-15.27624.29620.768
240.0421-0.07110.03530.5506-1.21233.068-0.13991.0369-0.3545-0.57570.43460.08271.3128-0.7314-0.29011.049-0.38270.01282.091-0.56650.6605-19.08819.368.376
257.6554-5.9922-2.04895.57114.52239.2403-0.16351.30790.5635-0.4170.3142-0.8455-0.70130.2249-0.14470.3498-0.17870.0141.09120.03640.4468-16.5240.09925.282
262.74631.3304-0.84510.90550.4094.6794-0.66112.0137-0.2541-0.55390.7463-0.1043-0.21650.4563-0.19470.6432-0.29060.14241.8966-0.20870.4043-14.63534.70313.509
270.32441.3317-1.04045.6252-4.38443.4218-0.36470.8878-0.3553-0.43790.23730.2792-1.4537-0.7515-0.17940.6461-0.2295-0.05051.58320.21350.374-28.48941.7921.915
286.88492.3205-3.88926.7206-2.22074.7442-0.00560.30510.3412-0.57890.5248-0.9539-0.97310.5282-0.47690.8613-0.58250.131.86790.06830.4782-10.0439.99612.005
290.8484-0.1229-1.58322.5589-1.02193.4644-0.47041.0251-0.0928-0.86870.39020.6319-0.594-0.8544-0.03270.8669-0.1542-0.13631.83730.3570.2829-28.47140.62716.189
301.448-2.64522.55618.1569-0.72119.2791-0.3448-0.21150.3554-0.10580.01770.891-1.2446-1.46350.29610.6610.0776-0.02331.53510.3350.4728-33.60245.49523.344
310.0686-0.01770.49111.59420.75523.4982-0.47551.8876-0.4256-0.82330.52830.1308-0.1688-0.61010.01020.7751-0.27370.11922.4005-0.50340.1714-16.71729.2410.704
326.26592.8511-1.26212.558-3.98669.3977-0.17191.1764-1.8016-0.76940.4709-1.19080.8789-0.6299-0.38010.6337-0.1650.0031.1428-0.4630.8798-26.1415.28422.438
332.2680.36440.16091.1728-0.17443.4221-0.0527-0.4413-0.05830.1635-0.0680.14-0.2856-0.74210.12730.27970.12880.03160.57520.00660.3097-12.55539.00158.014
343.02330.84760.7637.8722.99942.43880.7449-1.00070.88260.9303-0.60070.8751-1.1493-0.5127-0.09311.2137-0.00610.350.9891-0.23920.6658-1.37860.05778.052
358.11785.95992.5994.77873.44354.47860.05820.2663-0.20240.117-0.0004-0.31-0.23950.2177-0.09580.24830.07440.01680.1997-0.00050.285710.09346.79446.869
365.4530.87655.40230.13680.90035.3406-0.07631.2425-0.567-0.46080.0325-0.0680.05510.4180.07090.31210.02230.07830.5988-0.04720.3261-3.07236.20735.011
379.74541.33030.25026.9935-3.73245.65320.1647-0.3661.00410.09320.13540.4372-1.2528-0.7098-0.24140.30710.1018-0.03640.2088-0.01230.3331-1.7450.78451.278
388.65854.49045.44054.2365.85218.3357-0.10270.72910.7811-0.43790.04330.3533-0.789-0.20320.06260.51120.18270.01110.43430.13150.3246-3.953.06640.26
392.67151.153-0.3382.7355-0.59872.49540.3129-0.64310.39990.6714-0.20490.0872-0.87020.1313-0.04330.524-0.00110.06040.3933-0.10360.28836.35254.43459.661
401.8178-1.58411.9031.477-1.52119.25550.0318-1.09660.80231.2664-0.5324-1.1697-0.08420.66840.38081.0228-0.3275-0.20211.1-0.10150.61219.00561.63771.769
418.82872.65226.01397.59114.31875.01130.7763-2.29490.52332.3134-0.4037-1.22780.78990.361-0.37881.3173-0.3521-0.20291.5018-0.12390.760919.38457.39982.041
428.0461-2.7154.04932.0007-6.73035.08430.1002-0.23150.22620.63170.26170.007-1.2179-0.6587-0.35090.7591-0.0270.08770.5189-0.09180.4378.37162.2761.24
430.17970.06410.27220.30380.38150.60880.4328-1.37110.42831.1698-0.5879-0.3768-0.39460.3396-0.08891.9368-0.7342-0.1271.7745-0.3690.534717.74565.16883.932
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 44:215 )A44 - 215
2X-RAY DIFFRACTION2( CHAIN A AND RESID 216:258 )A216 - 258
3X-RAY DIFFRACTION3( CHAIN A AND RESID 259:492 )A259 - 492
4X-RAY DIFFRACTION4( CHAIN B AND RESID 1:17 )B1 - 17
5X-RAY DIFFRACTION5( CHAIN B AND RESID 18:111 )B18 - 111
6X-RAY DIFFRACTION6( CHAIN B AND RESID 112:193 )B112 - 193
7X-RAY DIFFRACTION7( CHAIN B AND RESID 194:214 )B194 - 214
8X-RAY DIFFRACTION8( CHAIN C AND RESID 1:25 )C1 - 25
9X-RAY DIFFRACTION9( CHAIN C AND RESID 26:32 )C26 - 32
10X-RAY DIFFRACTION10( CHAIN C AND RESID 33:48 )C33 - 48
11X-RAY DIFFRACTION11( CHAIN C AND RESID 49:61 )C49 - 61
12X-RAY DIFFRACTION12( CHAIN C AND RESID 62:137 )C62 - 137
13X-RAY DIFFRACTION13( CHAIN C AND RESID 138:174 )C138 - 174
14X-RAY DIFFRACTION14( CHAIN C AND RESID 175:198 )C175 - 198
15X-RAY DIFFRACTION15( CHAIN C AND RESID 199:214 )C199 - 214
16X-RAY DIFFRACTION16( CHAIN G AND RESID 44:64 )G44 - 64
17X-RAY DIFFRACTION17( CHAIN G AND RESID 65:98 )G65 - 98
18X-RAY DIFFRACTION18( CHAIN G AND RESID 99:115 )G99 - 115
19X-RAY DIFFRACTION19( CHAIN G AND RESID 116:202 )G116 - 202
20X-RAY DIFFRACTION20( CHAIN G AND RESID 203:235 )G203 - 235
21X-RAY DIFFRACTION21( CHAIN G AND RESID 236:245 )G236 - 245
22X-RAY DIFFRACTION22( CHAIN G AND RESID 246:255 )G246 - 255
23X-RAY DIFFRACTION23( CHAIN G AND RESID 256:273 )G256 - 273
24X-RAY DIFFRACTION24( CHAIN G AND RESID 274:287 )G274 - 287
25X-RAY DIFFRACTION25( CHAIN G AND RESID 288:301 )G288 - 301
26X-RAY DIFFRACTION26( CHAIN G AND RESID 324:378 )G324 - 378
27X-RAY DIFFRACTION27( CHAIN G AND RESID 379:385 )G379 - 385
28X-RAY DIFFRACTION28( CHAIN G AND RESID 386:398 )G386 - 398
29X-RAY DIFFRACTION29( CHAIN G AND RESID 399:431 )G399 - 431
30X-RAY DIFFRACTION30( CHAIN G AND RESID 432:444 )G432 - 444
31X-RAY DIFFRACTION31( CHAIN G AND RESID 445:474 )G445 - 474
32X-RAY DIFFRACTION32( CHAIN G AND RESID 475:491 )G475 - 491
33X-RAY DIFFRACTION33( CHAIN H AND RESID 1:109 )H1 - 109
34X-RAY DIFFRACTION34( CHAIN H AND RESID 110:213 )H110 - 213
35X-RAY DIFFRACTION35( CHAIN L AND RESID 1:25 )L1 - 25
36X-RAY DIFFRACTION36( CHAIN L AND RESID 26:32 )L26 - 32
37X-RAY DIFFRACTION37( CHAIN L AND RESID 33:48 )L33 - 48
38X-RAY DIFFRACTION38( CHAIN L AND RESID 49:61 )L49 - 61
39X-RAY DIFFRACTION39( CHAIN L AND RESID 62:137 )L62 - 137
40X-RAY DIFFRACTION40( CHAIN L AND RESID 138:150 )L138 - 150
41X-RAY DIFFRACTION41( CHAIN L AND RESID 151:163 )L151 - 163
42X-RAY DIFFRACTION42( CHAIN L AND RESID 164:174 )L164 - 174
43X-RAY DIFFRACTION43( CHAIN L AND RESID 175:213 )L175 - 213

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