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- PDB-3ghe: Crystal structure of anti-HIV-1 Fab 537-10D in complex with V3 pe... -

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Basic information

Entry
Database: PDB / ID: 3ghe
TitleCrystal structure of anti-HIV-1 Fab 537-10D in complex with V3 peptide MN
Components
  • Envelope glycoprotein
  • Fab 537-10D, heavy chain
  • Fab 537-10D, light chain
KeywordsIMMUNE SYSTEM / HIV / V3 LOOP / ANTIBODY-ANTIGEN INTERACTIONS / Envelope protein
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 speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKong, X.P. / Burke, V.J.
CitationJournal: Structure / Year: 2009
Title: Structural basis of the cross-reactivity of genetically related human anti-HIV-1 mAbs: implications for design of V3-based immunogens
Authors: Burke, V. / Williams, C. / Sukumaran, M. / Kim, S.S. / Li, H. / Wang, X.H. / Gorny, M.K. / Zolla-Pazner, S. / Kong, X.P.
History
DepositionMar 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Source and taxonomy / Category: pdbx_entity_src_syn / software
Item: _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.3Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Fab 537-10D, light chain
H: Fab 537-10D, heavy chain
P: Envelope glycoprotein


Theoretical massNumber of molelcules
Total (without water)50,0933
Polymers50,0933
Non-polymers00
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-27 kcal/mol
Surface area20590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.363, 71.322, 77.124
Angle α, β, γ (deg.)90.00, 104.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab 537-10D, light chain


Mass: 22911.236 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: B cell / Source: (natural) Homo sapiens (human)
#2: Antibody Fab 537-10D, heavy chain


Mass: 25433.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: B cell / Source: (natural) Homo sapiens (human)
#3: Protein/peptide Envelope glycoprotein


Mass: 1748.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P88403
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 296.15 K / pH: 7.5
Details: 20% PEG 4000, 5% Isoproponal, 0.1M Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 29, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.99→29.95 Å / Num. obs: 23276 / % possible obs: 73.1 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 31.8 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.08
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2 / Rsym value: 0.331 / % possible all: 8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CRYSTAL STRUCTURE OF 2557 FAB WITH V3 PEPTIDE NY5

Resolution: 2.4→29.95 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.241 875 4.6 %RANDOM
Rwork0.187 ---
obs0.187 18197 94.8 %-
all-19199 --
Solvent computationBsol: 43.64 Å2
Displacement parametersBiso mean: 34.58 Å2
Baniso -1Baniso -2Baniso -3
1-7.099 Å20 Å2-8.438 Å2
2---7.322 Å20 Å2
3---0.223 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3425 0 0 322 3747
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.37
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.03
RfactorNum. reflection% reflection
Rfree0.35 136 -
Rwork0.282 --
obs--82.8 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM

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