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- PDB-3q6g: Crystal structure of Fab of rhesus mAb 2.5B specific for quaterna... -

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Basic information

Entry
Database: PDB / ID: 3q6g
TitleCrystal structure of Fab of rhesus mAb 2.5B specific for quaternary neutralizing epitope of HIV-1 gp120
Components
  • Heavy chain of Fab of rhesus mAb 2.5B
  • Light chain of Fab of rhesus mAb 2.5B
KeywordsIMMUNE SYSTEM / Ig / neutralization of HIV-1 viruses / Quaternary epitope of HIV-1 gp120
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.902 Å
AuthorsSpurrier, B. / Sampson, J. / Totrov, M. / Li, H. / O'Neal, T. / William, C. / Robinson, J. / Gorny, M.K. / Zolla-Pazner, S. / Kong, X.P.
CitationJournal: Structure / Year: 2011
Title: Structural Analysis of Human and Macaque mAbs 2909 and 2.5B: Implications for the Configuration of the Quaternary Neutralizing Epitope of HIV-1 gp120.
Authors: Spurrier, B. / Sampson, J.M. / Totrov, M. / Li, H. / O'Neal, T. / Williams, C. / Robinson, J. / Gorny, M.K. / Zolla-Pazner, S. / Kong, X.P.
History
DepositionDec 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2013Group: Source and taxonomy

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Light chain of Fab of rhesus mAb 2.5B
H: Heavy chain of Fab of rhesus mAb 2.5B
M: Light chain of Fab of rhesus mAb 2.5B
I: Heavy chain of Fab of rhesus mAb 2.5B


Theoretical massNumber of molelcules
Total (without water)93,9224
Polymers93,9224
Non-polymers00
Water15,655869
1
L: Light chain of Fab of rhesus mAb 2.5B
H: Heavy chain of Fab of rhesus mAb 2.5B


Theoretical massNumber of molelcules
Total (without water)46,9612
Polymers46,9612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-24 kcal/mol
Surface area20710 Å2
MethodPISA
2
M: Light chain of Fab of rhesus mAb 2.5B
I: Heavy chain of Fab of rhesus mAb 2.5B


Theoretical massNumber of molelcules
Total (without water)46,9612
Polymers46,9612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-25 kcal/mol
Surface area20400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.836, 72.817, 88.898
Angle α, β, γ (deg.)90.00, 115.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Light chain of Fab of rhesus mAb 2.5B


Mass: 22180.354 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Macaca mulatta (Rhesus monkey)
#2: Antibody Heavy chain of Fab of rhesus mAb 2.5B


Mass: 24780.408 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Macaca mulatta (Rhesus monkey)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 869 / 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: 2.42 Å3/Da / Density % sol: 49.14 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 18% PEG 3350, 100 mM ammonium nitrate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-B11.0332
SYNCHROTRONNSLS X6A21
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 28, 2009 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
211
ReflectionResolution: 1.9→50 Å / Num. obs: 68825 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.85 / Net I/σ(I): 17.8
Reflection shellResolution: 1.9→1.97 Å / % possible all: 92.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.902→29.702 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 24.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 3482 5.06 %Random
Rwork0.1909 ---
obs0.193 68825 97.68 %-
all-68825 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.299 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.6607 Å2-0 Å20.3776 Å2
2---0.2947 Å20 Å2
3----0.3661 Å2
Refinement stepCycle: LAST / Resolution: 1.902→29.702 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6554 0 0 869 7423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076712
X-RAY DIFFRACTIONf_angle_d1.1239149
X-RAY DIFFRACTIONf_dihedral_angle_d13.6282362
X-RAY DIFFRACTIONf_chiral_restr0.0781049
X-RAY DIFFRACTIONf_plane_restr0.0051174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9019-1.96990.29473290.26185939X-RAY DIFFRACTION90
1.9699-2.04880.28173100.23036359X-RAY DIFFRACTION95
2.0488-2.1420.25113550.21326400X-RAY DIFFRACTION97
2.142-2.25490.26833440.21296550X-RAY DIFFRACTION98
2.2549-2.39610.26083590.20816577X-RAY DIFFRACTION99
2.3961-2.5810.27463520.216645X-RAY DIFFRACTION99
2.581-2.84060.25573520.20496669X-RAY DIFFRACTION100
2.8406-3.25120.22913320.18836712X-RAY DIFFRACTION100
3.2512-4.09440.19484000.16666697X-RAY DIFFRACTION100
4.0944-29.7060.19413490.16526786X-RAY DIFFRACTION99

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