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- PDB-4xml: Crystal structure of Fab of HIV-1 gp120 V3-specific human monoclo... -

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Basic information

Entry
Database: PDB / ID: 4xml
TitleCrystal structure of Fab of HIV-1 gp120 V3-specific human monoclonal antibody 2424
Components
  • Heavy chain of HIV-1 gp120 V3-specific human monoclonal antibody 2424
  • Light chain of HIV-1 gp120 V3-specific human monoclonal antibody 2424
KeywordsIMMUNE SYSTEM / HIV-1 gp120 / monoclonal antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.68 Å
AuthorsPan, R. / Kong, X.-P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI100151 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI082274 United States
CitationJournal: J.Virol. / Year: 2015
Title: Functional and Structural Characterization of Human V3-Specific Monoclonal Antibody 2424 with Neutralizing Activity against HIV-1 JRFL.
Authors: Kumar, R. / Pan, R. / Upadhyay, C. / Mayr, L. / Cohen, S. / Wang, X.H. / Balasubramanian, P. / Nadas, A. / Seaman, M.S. / Zolla-Pazner, S. / Gorny, M.K. / Kong, X.P. / Hioe, C.E.
History
DepositionJan 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2May 31, 2017Group: Other
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Light chain of HIV-1 gp120 V3-specific human monoclonal antibody 2424
H: Heavy chain of HIV-1 gp120 V3-specific human monoclonal antibody 2424


Theoretical massNumber of molelcules
Total (without water)47,2302
Polymers47,2302
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-22 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.592, 45.043, 74.778
Angle α, β, γ (deg.)90.00, 96.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Light chain of HIV-1 gp120 V3-specific human monoclonal antibody 2424


Mass: 23533.193 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Heavy chain of HIV-1 gp120 V3-specific human monoclonal antibody 2424


Mass: 23696.426 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 8000, Tris, glycerol / PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.68→50 Å / Num. obs: 13122 / % possible obs: 99.1 % / Redundancy: 3.2 % / Net I/σ(I): 11.5
Reflection shellResolution: 2.68→2.84 Å / Mean I/σ(I) obs: 1.98 / % possible all: 98.6

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementResolution: 2.68→47.862 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.17 / Phase error: 30.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.285 656 5 %
Rwork0.1995 --
obs0.2039 13118 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.68→47.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3287 0 0 33 3320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093368
X-RAY DIFFRACTIONf_angle_d1.2254575
X-RAY DIFFRACTIONf_dihedral_angle_d18.361206
X-RAY DIFFRACTIONf_chiral_restr0.049507
X-RAY DIFFRACTIONf_plane_restr0.005592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6796-2.88650.40081200.30152447X-RAY DIFFRACTION99
2.8865-3.17690.30611340.24882478X-RAY DIFFRACTION99
3.1769-3.63650.27271290.21312466X-RAY DIFFRACTION99
3.6365-4.5810.28411330.17242507X-RAY DIFFRACTION100
4.581-47.870.25721400.17592564X-RAY DIFFRACTION99

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