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- PDB-4oaw: Fab structure of anti-HIV gp120 V2 mAb 2158 -

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Basic information

Entry
Database: PDB / ID: 4oaw
TitleFab structure of anti-HIV gp120 V2 mAb 2158
Components
  • Heavy chain of Fab fragment of anti-HIV1 gp120 V2 mAb 2158
  • Light chain of Fab fragment of anti-HIV1 gp120 V2 mAb 2158
KeywordsIMMUNE SYSTEM / Ig / antibody / HIV-1 gp120
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSpurrier, B.R. / Kong, X.P.
CitationJournal: J.Virol. / Year: 2014
Title: Functional Implications of the Binding Mode of a Human Conformation-Dependent V2 Monoclonal Antibody against HIV.
Authors: Spurrier, B. / Sampson, J. / Gorny, M.K. / Zolla-Pazner, S. / Kong, X.P.
History
DepositionJan 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Light chain of Fab fragment of anti-HIV1 gp120 V2 mAb 2158
B: Heavy chain of Fab fragment of anti-HIV1 gp120 V2 mAb 2158
C: Light chain of Fab fragment of anti-HIV1 gp120 V2 mAb 2158
D: Heavy chain of Fab fragment of anti-HIV1 gp120 V2 mAb 2158
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,57712
Polymers96,8164
Non-polymers7618
Water2,954164
1
A: Light chain of Fab fragment of anti-HIV1 gp120 V2 mAb 2158
B: Heavy chain of Fab fragment of anti-HIV1 gp120 V2 mAb 2158
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7886
Polymers48,4082
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-82 kcal/mol
Surface area19580 Å2
MethodPISA
2
C: Light chain of Fab fragment of anti-HIV1 gp120 V2 mAb 2158
D: Heavy chain of Fab fragment of anti-HIV1 gp120 V2 mAb 2158
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7886
Polymers48,4082
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-70 kcal/mol
Surface area19590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.710, 73.710, 215.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Antibody Light chain of Fab fragment of anti-HIV1 gp120 V2 mAb 2158


Mass: 23355.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293 / Production host: homo sapiens (human)
#2: Antibody Heavy chain of Fab fragment of anti-HIV1 gp120 V2 mAb 2158


Mass: 25052.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293 / Production host: homo sapiens (human)
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

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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: 3.5 Å3/Da / Density % sol: 64.84 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 23.5% PEG 4K/0.17M ammonium sulfate/15% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 27, 2011
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→215 Å / Num. all: 32570 / Num. obs: 31988 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rsym value: 0.23 / Net I/σ(I): 5.6
Reflection shellResolution: 2.76→2.8 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.95 / % possible all: 98.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2QAD

2qad


Resolution: 2.8→54.831 Å / SU ML: 0.49 / σ(F): 1.96 / Phase error: 28.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2544 1623 5.07 %
Rwork0.1823 --
obs0.1859 31981 99.58 %
all-31981 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→54.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6786 0 42 164 6992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016974
X-RAY DIFFRACTIONf_angle_d1.3389482
X-RAY DIFFRACTIONf_dihedral_angle_d18.1832482
X-RAY DIFFRACTIONf_chiral_restr0.0491100
X-RAY DIFFRACTIONf_plane_restr0.0061194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.88240.39781460.32192528X-RAY DIFFRACTION99
2.8824-2.97550.36471340.29212517X-RAY DIFFRACTION100
2.9755-3.08180.32491450.26512541X-RAY DIFFRACTION99
3.0818-3.20520.32621440.23972523X-RAY DIFFRACTION100
3.2052-3.3510.34581420.2232545X-RAY DIFFRACTION100
3.351-3.52770.27881300.19222495X-RAY DIFFRACTION100
3.5277-3.74860.24231260.1882524X-RAY DIFFRACTION100
3.7486-4.0380.27251410.18252515X-RAY DIFFRACTION100
4.038-4.44420.23231200.14122563X-RAY DIFFRACTION100
4.4442-5.08690.18311270.12542544X-RAY DIFFRACTION100
5.0869-6.40740.21371450.14652511X-RAY DIFFRACTION100
6.4074-54.84120.1751230.15432552X-RAY DIFFRACTION99

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