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- PDB-4jo2: Crystal structure of rabbit mAb R56 Fab in complex with V3 crown ... -

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Basic information

Entry
Database: PDB / ID: 4jo2
TitleCrystal structure of rabbit mAb R56 Fab in complex with V3 crown of HIV-1 Consensus A gp120
Components
  • gp120
  • monoclonal anti-HIV-1 gp120 V3 antibody R56 heavy chain
  • monoclonal anti-HIV-1 gp120 V3 antibody R56 light chain
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / Ig / antibody / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


viral process / viral envelope
Similarity search - Function
Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesOryctolagus cuniculus (rabbit)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPan, R.M. / Kong, X.P.
CitationJournal: J.Virol. / Year: 2013
Title: Rabbit Anti-HIV-1 Monoclonal Antibodies Raised by Immunization Can Mimic the Antigen-Binding Modes of Antibodies Derived from HIV-1-Infected Humans.
Authors: Pan, R. / Sampson, J.M. / Chen, Y. / Vaine, M. / Wang, S. / Lu, S. / Kong, X.P.
History
DepositionMar 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: monoclonal anti-HIV-1 gp120 V3 antibody R56 light chain
H: monoclonal anti-HIV-1 gp120 V3 antibody R56 heavy chain
P: gp120
M: monoclonal anti-HIV-1 gp120 V3 antibody R56 light chain
I: monoclonal anti-HIV-1 gp120 V3 antibody R56 heavy chain
Q: gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,47512
Polymers94,2356
Non-polymers2406
Water8,629479
1
L: monoclonal anti-HIV-1 gp120 V3 antibody R56 light chain
H: monoclonal anti-HIV-1 gp120 V3 antibody R56 heavy chain
P: gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2386
Polymers47,1173
Non-polymers1203
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-60 kcal/mol
Surface area18850 Å2
MethodPISA
2
M: monoclonal anti-HIV-1 gp120 V3 antibody R56 light chain
I: monoclonal anti-HIV-1 gp120 V3 antibody R56 heavy chain
Q: gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2386
Polymers47,1173
Non-polymers1203
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-61 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.840, 74.350, 84.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody monoclonal anti-HIV-1 gp120 V3 antibody R56 light chain


Mass: 22782.014 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#2: Antibody monoclonal anti-HIV-1 gp120 V3 antibody R56 heavy chain


Mass: 21882.527 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#3: Protein/peptide gp120


Mass: 2452.747 Da / Num. of mol.: 2
Fragment: third variable region (V3) crown (UNP residues 30-52)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / References: UniProt: Q9YXH5
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 26% PEG6000, 1 M lithium chloride, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 6, 2010
RadiationMonochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→26.465 Å / Num. obs: 30171 / % possible obs: 99.72 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.127 / Rsym value: 0.161 / Net I/σ(I): 8.93
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4 % / Rmerge(I) obs: 0.607 / Mean I/σ(I) obs: 2.64 / Rsym value: 0.587 / % possible all: 89.9

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Processing

Software
NameVersionClassification
Blu-Icelikedata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→26.465 Å / SU ML: 0.38 / σ(F): 0 / Phase error: 23.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2654 1565 5.19 %RANDOM
Rwork0.1895 ---
all0.1934 51241 --
obs0.1934 30171 99.72 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.275 Å2 / ksol: 0.314 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4203 Å20 Å20.1222 Å2
2--1.0763 Å2-0 Å2
3----0.6561 Å2
Refinement stepCycle: LAST / Resolution: 2.5→26.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6330 0 6 479 6815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086478
X-RAY DIFFRACTIONf_angle_d1.1478836
X-RAY DIFFRACTIONf_dihedral_angle_d14.7172240
X-RAY DIFFRACTIONf_chiral_restr0.071054
X-RAY DIFFRACTIONf_plane_restr0.0051134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.58930.28341360.20082841X-RAY DIFFRACTION100
2.5893-2.69290.32441460.21922852X-RAY DIFFRACTION100
2.6929-2.81530.32031610.21492831X-RAY DIFFRACTION100
2.8153-2.96350.27211680.20522830X-RAY DIFFRACTION100
2.9635-3.14890.31121540.19722890X-RAY DIFFRACTION100
3.1489-3.39160.27711570.20392824X-RAY DIFFRACTION100
3.3916-3.73210.24131540.19272871X-RAY DIFFRACTION100
3.7321-4.27020.22971900.16422853X-RAY DIFFRACTION100
4.2702-5.37250.22431430.14982901X-RAY DIFFRACTION100
5.3725-26.46660.26931560.2052913X-RAY DIFFRACTION99

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