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- PDB-2pr4: Crystal Structure of Fab' from the HIV-1 Neutralizing Antibody 2F5 -

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Basic information

Entry
Database: PDB / ID: 2pr4
TitleCrystal Structure of Fab' from the HIV-1 Neutralizing Antibody 2F5
Components
  • nmAb 2F5 Fab' Heavy Chain
  • nmAb 2F5 Fab' light Chain
KeywordsVIRAL PROTEIN / nmAb 2F5 / gp41 / HIV
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsBryson, S. / Julien, J.-P. / Pai, E.F.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural details of HIV-1 recognition by the broadly neutralizing monoclonal antibody 2F5: epitope conformation, antigen-recognition loop mobility, and anion-binding site.
Authors: Julien, J.P. / Bryson, S. / Nieva, J.L. / Pai, E.F.
History
DepositionMay 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: nmAb 2F5 Fab' Heavy Chain
H: nmAb 2F5 Fab' light Chain


Theoretical massNumber of molelcules
Total (without water)48,3652
Polymers48,3652
Non-polymers00
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-22 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.600, 76.400, 94.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsLight chain interacts with the Heavy chain to form Fab' fragment.

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Components

#1: Antibody nmAb 2F5 Fab' Heavy Chain


Mass: 23363.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: Antibody nmAb 2F5 Fab' light Chain


Mass: 25001.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.5M Li2SO4, 15% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Oct 1, 1998
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. obs: 26917 / % possible obs: 92 % / Redundancy: 3.2 % / Biso Wilson estimate: 11.7 Å2 / Net I/σ(I): 15
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.313 / % possible all: 93

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Processing

Software
NameVersionClassification
DENZOdata reduction
AMoREphasing
CNS0.4refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→20 Å / σ(I): 0
RfactorNum. reflection% reflection
Rfree0.27 1282 -
Rwork0.24 --
obs-26304 89.4 %
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3269 0 0 266 3535
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_dihedral_angle_d27
X-RAY DIFFRACTIONx_improper_angle_d4.8
LS refinement shellResolution: 2.05→2.18 Å
RfactorNum. reflection% reflection
Rfree0.302 202 -
Rwork0.256 --
obs--94.2 %

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