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- PDB-3mlu: Crystal structure of anti-HIV-1 V3 Fab 2557 in complex with a ZAM... -

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Basic information

Entry
Database: PDB / ID: 3mlu
TitleCrystal structure of anti-HIV-1 V3 Fab 2557 in complex with a ZAM18 V3 peptide
Components
  • HIV-1 gp120 third variable region (V3) crown
  • Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab heavy chain
  • Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab light chain
KeywordsIMMUNE SYSTEM / human monoclonal antibody / Fab / HIV-1 / gp120 / third variable loop / antibody-antigen interaction
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
Envelope glycoprotein / Glycoprotein 120
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsKong, X.-P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Conserved structural elements in the V3 crown of HIV-1 gp120.
Authors: Jiang, X. / Burke, V. / Totrov, M. / Williams, C. / Cardozo, T. / Gorny, M.K. / Zolla-Pazner, S. / Kong, X.P.
History
DepositionApr 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab light chain
H: Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab heavy chain
P: HIV-1 gp120 third variable region (V3) crown


Theoretical massNumber of molelcules
Total (without water)49,8573
Polymers49,8573
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-33 kcal/mol
Surface area20280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.452, 43.167, 57.824
Angle α, β, γ (deg.)89.15, 86.25, 85.19
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab light chain


Mass: 23270.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: Antibody Human monoclonal anti-HIV-1 gp120 V3 antibody 2557 Fab heavy chain


Mass: 24191.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Protein/peptide HIV-1 gp120 third variable region (V3) crown


Mass: 2394.710 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human immunodeficiency virus 1 / References: UniProt: Q9J0Z7, UniProt: A0A0K0KAD3*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE FAB WERE MADE BY ENZYME DIGESTION, THEREFORE THE REAL ENDINGS OF THE CHAINS ...AUTHORS STATE THAT THE FAB WERE MADE BY ENZYME DIGESTION, THEREFORE THE REAL ENDINGS OF THE CHAINS ARE UNKNOWN.

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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: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 19% PEG 3350, 0.19 M CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 11, 2007
Details: a KOHZU double crystal monochromator with a sagittally focused second crystal. Two spherical mirrors, one will be rhodium coated. User choice of either mirror depending on the desired energy
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.77→50 Å / Num. obs: 10115 / % possible obs: 98.8 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Rmerge(I) obs% possible all
2.77-2.90.34898.3
2.9-3.020.27998.1
3.02-3.150.22698.5
3.15-3.320.16598.5
3.32-3.530.13398.5
3.53-3.80.11699
3.8-4.180.09498.9
4.18-4.790.08199
4.79-6.030.0899.4
6.03-500.0799.8

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.1_357refinement
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.77→35.167 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.78 / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.52 / σ(F): 1.97 / Phase error: 34.7 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.31 483 4.78 %
Rwork0.1961 --
obs0.2017 10104 97.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.436 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.7836 Å2-0.3355 Å21.31 Å2
2---0.9046 Å2-0.0007 Å2
3---0.121 Å2
Refinement stepCycle: LAST / Resolution: 2.77→35.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3411 0 0 123 3534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093500
X-RAY DIFFRACTIONf_angle_d1.2674762
X-RAY DIFFRACTIONf_dihedral_angle_d17.051247
X-RAY DIFFRACTIONf_chiral_restr0.077537
X-RAY DIFFRACTIONf_plane_restr0.006603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-2.90.34541620.22563057X-RAY DIFFRACTION93
3.167-3.98920.36771650.19163275X-RAY DIFFRACTION99
3.9892-35.16970.25341560.18123289X-RAY DIFFRACTION99

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