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- PDB-7s8h: Structure of Lassa virus glycoprotein bound to Fab 18.5C and Fab 36.1F -

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Basic information

Entry
Database: PDB / ID: 7s8h
TitleStructure of Lassa virus glycoprotein bound to Fab 18.5C and Fab 36.1F
Components
  • (Glycoprotein ...) x 2
  • 18.5C Fab Heavy Chain
  • 18.5C Fab Light Chain
  • 36.1F Fab Heavy Chain
  • 36.1F Fab Light Chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Lassa virus / pre-fusion glycoprotein / Fab fragment / antibody-mediated neutralization / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell Golgi membrane / receptor-mediated endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesLassa virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHastie, K.M. / Enriquez, A.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19A142790 United States
CitationJournal: Cell Rep / Year: 2022
Title: Delineating the mechanism of anti-Lassa virus GPC-A neutralizing antibodies.
Authors: Adrian S Enriquez / Tierra K Buck / Haoyang Li / Michael J Norris / Alex Moon-Walker / Michelle A Zandonatti / Stephanie S Harkins / James E Robinson / Luis M Branco / Robert F Garry / Erica ...Authors: Adrian S Enriquez / Tierra K Buck / Haoyang Li / Michael J Norris / Alex Moon-Walker / Michelle A Zandonatti / Stephanie S Harkins / James E Robinson / Luis M Branco / Robert F Garry / Erica Ollmann Saphire / Kathryn M Hastie /
Abstract: Lassa virus (LASV) is the etiologic agent of Lassa Fever, a hemorrhagic disease that is endemic to West Africa. During LASV infection, LASV glycoprotein (GP) engages with multiple host receptors for ...Lassa virus (LASV) is the etiologic agent of Lassa Fever, a hemorrhagic disease that is endemic to West Africa. During LASV infection, LASV glycoprotein (GP) engages with multiple host receptors for cell entry. Neutralizing antibodies against GP are rare and principally target quaternary epitopes displayed only on the metastable, pre-fusion conformation of GP. Currently, the structural features of the neutralizing GPC-A antibody competition group are understudied. Structures of two GPC-A antibodies presented here demonstrate that they bind the side of the pre-fusion GP trimer, bridging the GP1 and GP2 subunits. Complementary biochemical analyses indicate that antibody 25.10C, which is broadly specific, neutralizes by inhibiting binding of the endosomal receptor LAMP1 and also by blocking membrane fusion. The other GPC-A antibody, 36.1F, which is lineage-specific, prevents LAMP1 association only. These data illuminate a site of vulnerability on LASV GP and will guide efforts to elicit broadly reactive therapeutics and vaccines.
History
DepositionSep 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 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
A: Glycoprotein G1
H: 18.5C Fab Heavy Chain
L: 18.5C Fab Light Chain
B: 36.1F Fab Heavy Chain
C: 36.1F Fab Light Chain
a: Glycoprotein G2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,63116
Polymers137,8556
Non-polymers5,77610
Water1,15364
1
A: Glycoprotein G1
H: 18.5C Fab Heavy Chain
L: 18.5C Fab Light Chain
B: 36.1F Fab Heavy Chain
C: 36.1F Fab Light Chain
a: Glycoprotein G2
hetero molecules

A: Glycoprotein G1
H: 18.5C Fab Heavy Chain
L: 18.5C Fab Light Chain
B: 36.1F Fab Heavy Chain
C: 36.1F Fab Light Chain
a: Glycoprotein G2
hetero molecules

A: Glycoprotein G1
H: 18.5C Fab Heavy Chain
L: 18.5C Fab Light Chain
B: 36.1F Fab Heavy Chain
C: 36.1F Fab Light Chain
a: Glycoprotein G2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)430,89348
Polymers413,56418
Non-polymers17,32930
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area86360 Å2
ΔGint14 kcal/mol
Surface area151840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.058, 163.058, 173.548
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z

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Components

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Glycoprotein ... , 2 types, 2 molecules Aa

#1: Protein Glycoprotein G1 / GP1


Mass: 22927.971 Da / Num. of mol.: 1 / Mutation: G243C, Residues 256-259 mutated from RRLL to RRRR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lassa virus / Strain: Mouse/Sierra Leone/Josiah/1976 / Gene: GPC, GP-C / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P08669
#6: Protein Glycoprotein G2 / GP2


Mass: 19117.678 Da / Num. of mol.: 1 / Mutation: E329P, M332T, I350C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lassa virus / Strain: Mouse/Sierra Leone/Josiah/1976 / Gene: GPC, GP-C / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P08669

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Antibody , 4 types, 4 molecules HLBC

#2: Antibody 18.5C Fab Heavy Chain


Mass: 24309.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody 18.5C Fab Light Chain


Mass: 23654.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody 36.1F Fab Heavy Chain


Mass: 24174.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#5: Antibody 36.1F Fab Light Chain


Mass: 23671.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Sugars , 5 types, 10 molecules

#7: 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)-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
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#8: 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.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#9: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#10: 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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-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
#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.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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 , 1 types, 64 molecules

#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.85 Å3/Da / Density % sol: 56.83 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / Details: 0.1 M Tris, pH 8.0, 1.25 M LiCl and 15% PEG 8k

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 2.7→47.18 Å / Num. obs: 73503 / % possible obs: 99.92 % / Redundancy: 10 % / Biso Wilson estimate: 64.22 Å2 / CC1/2: 0.996 / Net I/σ(I): 9.53
Reflection shellResolution: 2.7→2.8 Å / Num. unique obs: 7267 / CC1/2: 0.26

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P91
Resolution: 2.7→47.18 Å / SU ML: 0.4668 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 29.6406
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: The number of reflections in the test set (3601) was counted after merging Friedel pairs. The numbers of test set reflections in the various resolution shells were counted in the unmerged ...Details: The number of reflections in the test set (3601) was counted after merging Friedel pairs. The numbers of test set reflections in the various resolution shells were counted in the unmerged data, and thus add up to a larger number.
RfactorNum. reflection% reflection
Rfree0.2508 3601 -
Rwork0.2175 134741 -
obs-73503 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.91 Å2
Refinement stepCycle: LAST / Resolution: 2.7→47.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9376 0 384 64 9824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00519973
X-RAY DIFFRACTIONf_angle_d0.764113545
X-RAY DIFFRACTIONf_chiral_restr0.04461602
X-RAY DIFFRACTIONf_plane_restr0.00541678
X-RAY DIFFRACTIONf_dihedral_angle_d9.03321528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.730.39762080.36114446X-RAY DIFFRACTION100
2.73-2.760.41472340.354574X-RAY DIFFRACTION99.98
2.76-2.80.37992590.35494447X-RAY DIFFRACTION99.94
2.8-2.830.38232480.33784461X-RAY DIFFRACTION99.98
2.83-2.870.40752160.34654542X-RAY DIFFRACTION99.98
2.87-2.910.34741800.34264591X-RAY DIFFRACTION99.94
2.91-2.950.34971880.33394459X-RAY DIFFRACTION99.98
2.95-2.990.36712180.32084450X-RAY DIFFRACTION99.98
2.99-3.040.3372060.31984572X-RAY DIFFRACTION99.98
3.04-3.090.37242470.31414506X-RAY DIFFRACTION99.98
3.09-3.140.35222120.30354479X-RAY DIFFRACTION99.94
3.14-3.20.37112100.31374500X-RAY DIFFRACTION99.98
3.2-3.260.30992060.2774558X-RAY DIFFRACTION100
3.26-3.330.2692740.25264422X-RAY DIFFRACTION100
3.33-3.40.28562720.23034470X-RAY DIFFRACTION100
3.4-3.480.25322600.22064434X-RAY DIFFRACTION99.98
3.48-3.570.25212200.20874512X-RAY DIFFRACTION100
3.57-3.660.23962320.19654496X-RAY DIFFRACTION100
3.66-3.770.23982360.19794522X-RAY DIFFRACTION100
3.77-3.890.22852350.18974451X-RAY DIFFRACTION99.81
3.89-4.030.17592820.16234446X-RAY DIFFRACTION100
4.03-4.190.18832300.16284512X-RAY DIFFRACTION99.96
4.19-4.380.22232380.1374460X-RAY DIFFRACTION99.98
4.39-4.620.18132760.13834451X-RAY DIFFRACTION99.98
4.62-4.90.17762440.13774469X-RAY DIFFRACTION100
4.91-5.280.17132690.1484472X-RAY DIFFRACTION99.83
5.28-5.810.18992080.17174539X-RAY DIFFRACTION100
5.81-6.650.24451980.18914489X-RAY DIFFRACTION99.94
6.65-8.370.20972280.18464488X-RAY DIFFRACTION99.94
8.38-47.180.22472190.19114523X-RAY DIFFRACTION99.6
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.704224530722.19540155158-0.1864464405041.77568363251-0.4572800162282.06815986275-0.1937034400220.8907706592660.332159835476-0.4003901055110.100390967408-0.191569885656-0.06300874430330.4557430297590.08126268404950.4452245407980.0095887104388-0.02475308946240.9930620585380.04351244058460.716940422965-24.8859.36142.605
21.755041753461.24259449426-0.01784345715332.60769188744-1.181044276172.476924780030.155838490967-1.048125410560.09729996483030.264070490246-0.152107855868-0.2100714653970.1551278264580.613187623844-0.01983792947250.5506590146950.0286185126860.03726308541751.60807272074-0.2154420191140.7480036651097.85564.91157.625
31.4381401737-0.859107132831-0.7807362890743.010023292021.325402933162.25455812458-0.06394604380570.0979873085422-0.0379408261297-0.2706038264850.122760624153-0.1621815772030.0359092865660.0503198517378-0.05167386917170.4473889953990.00156913184623-0.00667369518740.3353131118870.003393205220430.414974485737-60.25615.10715.176
41.56623221650.02349333702060.02301081447232.14543669463-0.6408571355712.56787224935-0.1485963385770.0499495755373-0.333896119811-0.5252246443110.2736907497990.157932487950.882932996926-0.201323379353-0.1140807630590.8762086080540.004854629836030.01833965774280.4737826539330.005267862726220.58984992834-60.176-20.86212.52
51.03499152854-1.56863098636-0.5396497109024.36805973583-0.3685854068542.17957450215-0.360626080695-0.414054521835-0.2599599287280.8536354826540.2785095653010.3543756592320.3934396702380.07833634072760.07346960277010.6609150065960.1605920925620.06903416514290.4049649562760.0436844265670.476543874376-65.1499.02735.054
61.7669344006-0.416685430987-0.4772240342112.54660664039-0.8574431574093.16016259211-0.226876954242-0.145179360429-0.1911797312080.1285409404350.0472288564924-0.05657656557080.566578021840.6259706921770.09596335506120.8108498065420.233511309540.05056538418020.5717939219430.06744699623330.607235093648-51.778-22.73426.637
70.8875880468860.0221007665098-0.6923928361840.914226324894-0.233766667042.29948017471-0.0790496759683-0.180903274715-0.06694107462070.1428508641850.0801867156066-0.1131663209120.322202738732-0.04561613029750.001274918907540.384523482260.000388159518018-0.04673689495020.379436058649-0.003442082231750.38773319733-62.63941.02757.996
80.691847437609-0.0645175244713-0.1574728879782.177677203390.1146009323071.75344803435-0.002703721964640.08638218396570.100845399827-0.181281699104-0.0500261172277-0.04177238038490.005142869917270.0197734226880.01874289348690.285763910697-0.0168982289601-0.008239446376120.2794780663060.02185931881690.359406478584-64.53447.54632.673
92.706585669961.176609130140.05376020451370.7589841939150.01900599298560.9842521979290.176522712815-0.62398083381-0.3325788938880.145455387908-0.130911736794-0.287855763360.1521460026580.32658733155-0.01225708458360.4328011369130.0482007150767-0.0980151852760.9067805800880.02091331188020.660113181184-29.47449.61361.681
101.77889535054-1.094279672940.8866440442872.50236827597-0.6281243716893.420120127620.305900661017-1.635954916760.4334430472050.3948625573620.0859515862320.458424797633-0.926271833515-0.148762027116-0.4030192438880.810669648098-0.1123779404660.1690423980771.88541474337-0.2742864996570.723024844916-1.74769.37870.221
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND RESID 2:109 )C2 - 109
2X-RAY DIFFRACTION2( CHAIN C AND RESID 110:216 )C110 - 216
3X-RAY DIFFRACTION3( CHAIN H AND RESID 1:122 )H1 - 122
4X-RAY DIFFRACTION4( CHAIN H AND RESID 123:224 )H123 - 224
5X-RAY DIFFRACTION5( CHAIN L AND RESID 1:107 )L1 - 107
6X-RAY DIFFRACTION6( CHAIN L AND RESID 108:214 )L108 - 214
7X-RAY DIFFRACTION7( CHAIN A AND RESID 59:255 )A59 - 255
8X-RAY DIFFRACTION8( CHAIN a AND RESID 260:422 )a260 - 422
9X-RAY DIFFRACTION9( CHAIN B AND RESID 2:128 )B2 - 128
10X-RAY DIFFRACTION10( CHAIN B AND RESID 129:226 )B129 - 226

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