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- PDB-6u3z: Structure of VD20_5A4 Fab -

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Basic information

Entry
Database: PDB / ID: 6u3z
TitleStructure of VD20_5A4 Fab
Components
  • V20_5A4 Heavy Chain
  • V20_5A4 Light Chain
KeywordsIMMUNE SYSTEM / Fab / Antibody / HIV
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION / PRASEODYMIUM ION
Function and homology information
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99002311102 Å
AuthorsDionne, G. / Shapiro, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)1P01AI104722-01A1 United States
CitationJournal: J.Exp.Med. / Year: 2020
Title: Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses.
Authors: Phad, G.E. / Pushparaj, P. / Tran, K. / Dubrovskaya, V. / Adori, M. / Martinez-Murillo, P. / Vazquez Bernat, N. / Singh, S. / Dionne, G. / O'Dell, S. / Bhullar, K. / Narang, S. / Sorini, C. ...Authors: Phad, G.E. / Pushparaj, P. / Tran, K. / Dubrovskaya, V. / Adori, M. / Martinez-Murillo, P. / Vazquez Bernat, N. / Singh, S. / Dionne, G. / O'Dell, S. / Bhullar, K. / Narang, S. / Sorini, C. / Villablanca, E.J. / Sundling, C. / Murrell, B. / Mascola, J.R. / Shapiro, L. / Pancera, M. / Martin, M. / Corcoran, M. / Wyatt, R.T. / Karlsson Hedestam, G.B.
History
DepositionAug 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.journal_volume / _citation.year ..._citation.journal_volume / _citation.year / _citation_author.identifier_ORCID / _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: V20_5A4 Heavy Chain
B: V20_5A4 Light Chain
C: V20_5A4 Heavy Chain
D: V20_5A4 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,29413
Polymers95,6764
Non-polymers6189
Water5,080282
1
A: V20_5A4 Heavy Chain
B: V20_5A4 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0714
Polymers47,8382
Non-polymers2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-27 kcal/mol
Surface area19020 Å2
MethodPISA
2
C: V20_5A4 Heavy Chain
D: V20_5A4 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2239
Polymers47,8382
Non-polymers3857
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-62 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.207, 108.733, 55.418
Angle α, β, γ (deg.)90.0, 105.775, 90.0
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Antibody , 2 types, 4 molecules ACBD

#1: Antibody V20_5A4 Heavy Chain


Mass: 24666.510 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#2: Antibody V20_5A4 Light Chain


Mass: 23171.564 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)

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Non-polymers , 5 types, 291 molecules

#3: Chemical ChemComp-PR / PRASEODYMIUM ION / Praseodymium


Mass: 140.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Pr
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30% PEG3000, 0.2 M sodium chloride, 0.1 M Tris, pH 7, 0.01 M praseodymium(III) acetate hydrate, cryoprotectant: 26% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2017
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.99→84.31 Å / Num. obs: 67170 / % possible obs: 98.3 % / Redundancy: 3 % / Biso Wilson estimate: 37.9199020356 Å2 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.065 / Rrim(I) all: 0.117 / Net I/σ(I): 7.9
Reflection shellResolution: 1.99→2.061 Å / Redundancy: 3.1 % / Rmerge(I) obs: 1.198 / Mean I/σ(I) obs: 1.42 / Num. unique obs: 6800 / CC1/2: 0.212 / % possible all: 98.55

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 5F9W, 5DD5, 2BX5
Resolution: 1.99002311102→84.3040636766 Å / SU ML: 0.274506202631 / Cross valid method: FREE R-VALUE / σ(F): 1.33534688718 / Phase error: 27.1519359668
RfactorNum. reflection% reflection
Rfree0.236317856463 3282 4.88778351974 %
Rwork0.198942080158 63865 -
obs0.200763057575 67147 98.1107539451 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.2163183524 Å2
Refinement stepCycle: LAST / Resolution: 1.99002311102→84.3040636766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6568 0 27 282 6877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005280487445926754
X-RAY DIFFRACTIONf_angle_d0.9682966253479199
X-RAY DIFFRACTIONf_chiral_restr0.03568510158421052
X-RAY DIFFRACTIONf_plane_restr0.004257894089791168
X-RAY DIFFRACTIONf_dihedral_angle_d12.18525605362385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.999-2.01970.3157520231221550.3304963488412746X-RAY DIFFRACTION98.3056590986
2.0197-2.05130.3669886717741560.3205028769952790X-RAY DIFFRACTION98.4954864594
2.0513-2.08490.3433371108251410.3162874295952731X-RAY DIFFRACTION98.7960096319
2.0849-2.12090.3531184238751460.3233720160892802X-RAY DIFFRACTION98.3650316984
2.1209-2.15940.3547261840351370.3107165609222741X-RAY DIFFRACTION97.460209956
2.1594-2.2010.3343130258771410.304822665172749X-RAY DIFFRACTION97.0775948942
2.201-2.24590.337560796741420.2897674629222745X-RAY DIFFRACTION97.2381273156
2.2459-2.29480.3215408381971430.2898629430932798X-RAY DIFFRACTION99.090296496
2.2948-2.34810.3234397919411170.2814032041992804X-RAY DIFFRACTION98.8494077834
2.3481-2.40690.2974336364341440.2719982633922804X-RAY DIFFRACTION98.8266845458
2.4069-2.47190.2697503930291380.2671574336852777X-RAY DIFFRACTION98.5796415286
2.4719-2.54470.3237375177881380.2422493558362802X-RAY DIFFRACTION98.7239758227
2.5447-2.62680.2778548508491280.2379781324072803X-RAY DIFFRACTION98.5872855701
2.6268-2.72070.2512626691191570.2181754844532779X-RAY DIFFRACTION98.7554658594
2.7207-2.82970.2670816922541570.2148399349922761X-RAY DIFFRACTION98.7144790257
2.8297-2.95840.2353249655311390.2094232261952783X-RAY DIFFRACTION98.1525025193
2.9584-3.11440.2629828238891330.1958962473312762X-RAY DIFFRACTION96.9524447421
3.1144-3.30960.2435489506791510.190325422732725X-RAY DIFFRACTION96.2516733601
3.3096-3.56510.2150190423561340.1777799766262771X-RAY DIFFRACTION98.1087470449
3.5651-3.92390.1618468667351260.1694929713472803X-RAY DIFFRACTION97.9598662207
3.9239-4.49160.1952496720761490.1494286382972763X-RAY DIFFRACTION97.5871313673
4.4916-5.65880.1868309214391420.1431214238612806X-RAY DIFFRACTION98.0705256154
5.6588-84.30.1970321793971680.1597239020232820X-RAY DIFFRACTION97.7109221714

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