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- PDB-5uty: Crystal Structure of a Stabilized DS-SOSIP.mut4 BG505 gp140 HIV-1... -

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Basic information

Entry
Database: PDB / ID: 5uty
TitleCrystal Structure of a Stabilized DS-SOSIP.mut4 BG505 gp140 HIV-1 Env Trimer, Containing Mutations I201C-P433C (DS), L154M, N300M, N302M, T320L in Complex with Human Antibodies PGT122 and 35O22 at 4.1 Angstrom
Components
  • (HIV-1 BG505 strain Env ...) x 2
  • 35O22 Fab heavy chain
  • 35O22 Fab light chain
  • PGT122 Fab heavy chain
  • PGT122 Fab light chain
KeywordsVIRAL PROTEIN/immune system / HIV-1 Env / Stabilized Env / Near-native mimic of the viral spike / VIRAL PROTEIN-immune system complex
Function / homology
Function and homology information


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 / viral envelope / virion attachment to host cell / host cell plasma membrane ...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 / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / identical protein binding / 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
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.412 Å
AuthorsXu, K. / Chuang, G.-Y. / Pancera, M. / Kwong, P.D.
CitationJournal: J. Virol. / Year: 2017
Title: Structure-Based Design of a Soluble Prefusion-Closed HIV-1 Env Trimer with Reduced CD4 Affinity and Improved Immunogenicity.
Authors: Chuang, G.Y. / Geng, H. / Pancera, M. / Xu, K. / Cheng, C. / Acharya, P. / Chambers, M. / Druz, A. / Tsybovsky, Y. / Wanninger, T.G. / Yang, Y. / Doria-Rose, N.A. / Georgiev, I.S. / Gorman, ...Authors: Chuang, G.Y. / Geng, H. / Pancera, M. / Xu, K. / Cheng, C. / Acharya, P. / Chambers, M. / Druz, A. / Tsybovsky, Y. / Wanninger, T.G. / Yang, Y. / Doria-Rose, N.A. / Georgiev, I.S. / Gorman, J. / Joyce, M.G. / O'Dell, S. / Zhou, T. / McDermott, A.B. / Mascola, J.R. / Kwong, P.D.
History
DepositionFeb 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: HIV-1 BG505 strain Env gp41
D: 35O22 Fab heavy chain
E: 35O22 Fab light chain
G: HIV-1 BG505 strain Env gp120
H: PGT122 Fab heavy chain
L: PGT122 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,20228
Polymers171,0866
Non-polymers11,11622
Water00
1
B: HIV-1 BG505 strain Env gp41
D: 35O22 Fab heavy chain
E: 35O22 Fab light chain
G: HIV-1 BG505 strain Env gp120
H: PGT122 Fab heavy chain
L: PGT122 Fab light chain
hetero molecules

B: HIV-1 BG505 strain Env gp41
D: 35O22 Fab heavy chain
E: 35O22 Fab light chain
G: HIV-1 BG505 strain Env gp120
H: PGT122 Fab heavy chain
L: PGT122 Fab light chain
hetero molecules

B: HIV-1 BG505 strain Env gp41
D: 35O22 Fab heavy chain
E: 35O22 Fab light chain
G: HIV-1 BG505 strain Env gp120
H: PGT122 Fab heavy chain
L: PGT122 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)546,60784
Polymers513,25818
Non-polymers33,34966
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_415-y-1,x-y-4,z1
crystal symmetry operation3_845-x+y+3,-x-1,z1
Unit cell
Length a, b, c (Å)131.447, 131.447, 312.348
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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HIV-1 BG505 strain Env ... , 2 types, 2 molecules BG

#1: Protein HIV-1 BG505 strain Env gp41 / Envelope glycoprotein gp160


Mass: 17146.482 Da / Num. of mol.: 1 / Fragment: UNP residues 509-661
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6
#4: Protein HIV-1 BG505 strain Env gp120 / Envelope glycoprotein gp160


Mass: 56622.668 Da / Num. of mol.: 1 / Fragment: UNP residues 29-505
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6

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Antibody , 4 types, 4 molecules DEHL

#2: Antibody 35O22 Fab heavy chain


Mass: 26170.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody 35O22 Fab light chain


Mass: 23318.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody PGT122 Fab heavy chain


Mass: 25434.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#6: Antibody PGT122 Fab light chain


Mass: 22392.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 7 types, 22 molecules

#7: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-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
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 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]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#9: 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)-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]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_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]{}}}}}LINUCSPDB-CARE
#10: 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.: 9
Source method: isolated from a genetically manipulated source
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
#11: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-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]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/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)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#12: 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-(1-6)]alpha-D-mannopyranose-(1-6)]beta-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
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-j1_h2-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-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]{}}}}}}LINUCSPDB-CARE
#13: 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.: 8
Source method: isolated from a genetically manipulated source
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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Details

Has protein modificationY
Sequence detailsAuthors state that the first 30 residues in chain G is secretion signal sequence.

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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: 4.54 Å3/Da / Density % sol: 72.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 10.5% PEG 4000, 0.2M AmSO4, 0.1M NaoAc pH 4.6 / PH range: 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 4, 2016
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 25676 / % possible obs: 61 % / Redundancy: 7.8 % / Biso Wilson estimate: 86.58 Å2 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.053 / Rrim(I) all: 0.158 / Χ2: 1.186 / Net I/σ(I): 5.5 / Num. measured all: 199781
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.4-3.522.51.1360.3450.6181.3050.57217.4
3.52-3.663.91.1490.650.5121.2680.6125.1
3.66-3.834.91.2480.5670.5181.3580.6433.9
3.83-4.035.81.0140.7460.3971.0930.68141.3
4.03-4.286.50.5550.9620.2090.5950.78550
4.28-4.616.70.3690.9730.1370.3950.8661
4.61-5.086.70.2810.9780.1040.3010.84481.7
5.08-5.818.90.3140.9880.1090.3330.82999.5
5.81-7.3210.40.2180.9940.0710.2290.969100
7.32-509.90.070.9970.0240.0742.41799.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data collection
PHASERphasing
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TVP

4tvp


Resolution: 3.412→41.481 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 35.27 / Stereochemistry target values: ML
Details: Author state that the overall resolution was determined as follows: it is the highest resolution for which the completeness was greater than 50% and the I/sigmaI was greater than 2.0. ...Details: Author state that the overall resolution was determined as follows: it is the highest resolution for which the completeness was greater than 50% and the I/sigmaI was greater than 2.0. Crystal diffraction data were then assessed for anisotropy through use of the Diffraction Anisotropy Server (http://services.mbi.ucla.edu/anisoscale/), which indicates the resolution at which F/sigma drops below 3.0 along a, b, and c axes; for the two lattices, these were 4.9 A, 4.9 A , 3.4 A. Because we sought to use as much of the data as possible for refinement, we used the overall resolution described above to define the resolution of the a and b axes, with the resolution limit for the c axis defined by the Diffraction Anisotropy Server.
RfactorNum. reflection% reflection
Rfree0.2882 1269 5.29 %
Rwork0.2412 --
obs0.2437 24010 57.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.412→41.481 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11285 0 735 0 12020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412380
X-RAY DIFFRACTIONf_angle_d0.86116971
X-RAY DIFFRACTIONf_dihedral_angle_d15.4927364
X-RAY DIFFRACTIONf_chiral_restr0.0492067
X-RAY DIFFRACTIONf_plane_restr0.0052064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4123-3.54880.4536150.3431226X-RAY DIFFRACTION5
3.5488-3.71030.4268470.3359705X-RAY DIFFRACTION17
3.7103-3.90570.3554770.31861306X-RAY DIFFRACTION30
3.9057-4.15020.37731050.2841875X-RAY DIFFRACTION43
4.1502-4.47030.32151590.25412393X-RAY DIFFRACTION55
4.4703-4.91950.27871690.23233189X-RAY DIFFRACTION73
4.9195-5.62990.29642460.23464254X-RAY DIFFRACTION98
5.6299-7.08730.30482450.26924367X-RAY DIFFRACTION100
7.0873-41.48380.22912060.2114426X-RAY DIFFRACTION100
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)
10.0337-0.0677-0.00920.0786-0.00960.0191-0.0234-0.0233-0.03260.04370.04810.0029-0.0565-0.01410.10360.10460.17270.03150.08770.2176-0.0219213.5685-201.8889-25.6191
20.1191-0.0346-0.0020.0611-0.04170.0858-0.0429-0.10320.02340.01960.10330.0204-0.0326-0.03630.11550.02610.0268-0.01250.04330.24870.1806204.7318-190.098-18.4359
30.019-0.0085-0.0070.0069-0.00390.007-0.05640.05410.0441-0.00370.03220.0424-0.07090.064-0.01110.8309-0.05650.21840.63170.44270.6345224.5051-186.287-36.6193
40.00330.0131-0.00130.1053-0.02930.02970.0786-0.06630.00760.1148-0.0095-0.075-0.11340.02180.00370.4577-0.0820.01120.32560.35480.3353213.1969-179.856-31.8871
50.02080.022-0.00740.0164-0.00670.00380.0175-0.00250.07390.05160.02250.0843-0.0927-0.0676-0.00011.05380.12730.16010.96790.2011.3515257.2865-205.9629-30.7993
60.00970.01060.00620.01540.00750.0059-0.10930.02170.0683-0.0897-0.0797-0.01370.0048-0.00270.00010.96780.01270.20171.17460.20570.5156245.8569-204.5049-36.4129
70.01530.01370.00410.01730.00410.00380.09910.0336-0.1080.15120.00740.0803-0.07380.03970.00381.0540.20250.20341.05830.41290.7619242.1283-208.9732-30.5004
80.02470.0424-0.03970.064-0.0660.0587-0.03830.0025-0.0172-0.02380.00540.007-0.0098-0.02040.0120.68020.58670.17110.83980.46270.9735249.1681-207.334-37.8979
90.00250.0022-0.008-0.0021-0.0080.01570.14460.0515-0.07610.1070.1713-0.234-0.0169-0.02470.00020.63110.26-0.09991.06640.18870.7633258.6165-202.2842-35.996
100.01560.0076-0.00770.0049-0.00530.00080.09980.04420.04160.02160.0719-0.0419-0.01750.01930.00011.9364-0.0041-0.11881.95730.1492.421275.3945-182.0722-34.2349
110.0104-0.00030.00980.001-0.00290.00910.16250.0160.0867-0.01940.00350.1102-0.01890.157-0.00011.69790.2845-0.06932.0993-0.24411.9744269.6798-191.0273-34.4763
120.0006-0.0007-0.00060.00070.00090.00120.00760.008-0.0006-0.01040.02960.00980.00060.0133-02.84690.08340.00422.8373-0.17122.8859270.7331-172.7943-25.3962
130.0041-00.00270.00040.0007-0.0007-0.0489-0.00510.08460.0092-0.0273-0.0377-0.0240.0288-00.84270.2201-0.02051.22970.17441.3029271.2648-193.346-23.9677
140.00220.00230.00090.0010.00110.00060.0136-0.0209-0.0191-0.00840.03380.0141-0.0122-0.0109-03.228-0.13350.01353.16920.00213.1385280.3592-170.6521-31.9448
150.0468-0.014-0.04590.02160.01130.0216-0.0449-0.00530.05160.1341-0.161-0.0835-0.15740.218500.723-0.0910.15121.53080.39230.8755243.3716-193.3556-52.8373
160.01930.0205-0.01330.0182-0.01450.0038-0.11370.06370.00790.13050.0946-0.0061-0.13810.2344-01.3306-0.1198-0.06011.38430.1271.9182279.9672-185.3432-46.7069
170.00120.0011-0.04560.11350.05070.1845-0.3072-0.0092-0.07530.2672-0.2113-0.41980.22080.2173-0.55370.1601-0.31670.26120.39980.7482-0.3795213.0954-202.104312.2234
180.03960.1604-0.02930.067-0.07310.1323-0.3509-0.2269-0.07780.3050.0976-0.44060.23620.6286-0.1424-0.0552-0.29580.50390.2770.87980.0501226.2031-207.252910.8498
190.15520.03250.02550.00750.01610.0112-0.0644-0.15630.03090.1288-0.1313-0.1550.09060.0809-0.13160.5869-0.18120.0940.66860.44830.3403235.1104-236.487262.5452
200.0425-0.0039-0.03810.0048-0.01860.0047-0.00340.1570.052-0.2248-0.082-0.2121-0.04120.06270.06960.7743-0.2611-0.09130.58980.67230.3266231.9658-234.951461.169
210.00620.0061-0.00130.0545-0.0230.06190.0007-0.0866-0.1281-0.05490.0219-0.12050.14040.08610.04950.4837-0.09630.02460.54550.37850.7146223.1738-258.19481.0991
220.0125-0.00370.01150.00170.00060.00980.10980.03260.0243-0.0537-0.0028-0.06350.00580.0646-01.04880.2915-0.17881.04370.25621.1141231.7251-262.913483.8386
230.01850.02650.00170.0308-0.02340.00720.01050.0162-0.04970.1237-0.0519-0.14970.20580.1147-0.09790.46750.0875-0.11670.33450.40860.6693216.7861-241.332349.1013
240.01610.0342-0.03820.06330.02360.1246-0.0996-0.12390.08610.0167-0.2342-0.02570.03080.0209-0.1583-0.055-0.0868-0.03580.55830.13430.6952209.8356-258.455983.0068
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 517 through 569 )
2X-RAY DIFFRACTION2chain 'B' and (resid 570 through 605 )
3X-RAY DIFFRACTION3chain 'B' and (resid 606 through 627 )
4X-RAY DIFFRACTION4chain 'B' and (resid 628 through 659 )
5X-RAY DIFFRACTION5chain 'D' and (resid 1 through 20 )
6X-RAY DIFFRACTION6chain 'D' and (resid 21 through 52 )
7X-RAY DIFFRACTION7chain 'D' and (resid 52A through 77 )
8X-RAY DIFFRACTION8chain 'D' and (resid 78 through 100D)
9X-RAY DIFFRACTION9chain 'D' and (resid 100E through 118 )
10X-RAY DIFFRACTION10chain 'D' and (resid 119 through 145 )
11X-RAY DIFFRACTION11chain 'D' and (resid 146 through 182 )
12X-RAY DIFFRACTION12chain 'D' and (resid 183 through 194 )
13X-RAY DIFFRACTION13chain 'D' and (resid 195 through 210 )
14X-RAY DIFFRACTION14chain 'D' and (resid 211 through 224 )
15X-RAY DIFFRACTION15chain 'E' and (resid 2 through 106 )
16X-RAY DIFFRACTION16chain 'E' and (resid 106A through 210 )
17X-RAY DIFFRACTION17chain 'G' and (resid 31 through 235 )
18X-RAY DIFFRACTION18chain 'G' and (resid 236 through 505 )
19X-RAY DIFFRACTION19chain 'H' and (resid 1 through 59 )
20X-RAY DIFFRACTION20chain 'H' and (resid 60 through 122 )
21X-RAY DIFFRACTION21chain 'H' and (resid 123 through 182 )
22X-RAY DIFFRACTION22chain 'H' and (resid 183 through 211 )
23X-RAY DIFFRACTION23chain 'L' and (resid 8 through 102 )
24X-RAY DIFFRACTION24chain 'L' and (resid 103 through 210 )

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