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- PDB-6w73: Fab Structure of CD4 Binding Site (CD4bs) Huamn Monoclonal Antibo... -

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Basic information

Entry
Database: PDB / ID: 6w73
TitleFab Structure of CD4 Binding Site (CD4bs) Huamn Monoclonal Antibody HmAb64
Components
  • HmAb64 fab heavy chain
  • HmAb64 fab light chain
KeywordsIMMUNE SYSTEM / HIV-1 gp120 / antibody / IgG
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKong, X. / Pan, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI100151 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI145655 United States
CitationJournal: To Be Published
Title: A CD4 Binding Site (CD4bs) Monoclonal Antibody Elicited from A Human Volunteer Immunized by a DNA Prime/Protein Boost gp120 HIV Vaccine
Authors: Kong, X. / Pan, R.
History
DepositionMar 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: HmAb64 fab light chain
H: HmAb64 fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4584
Polymers47,3782
Non-polymers802
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-36 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.790, 59.352, 75.571
Angle α, β, γ (deg.)90.000, 96.215, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Antibody HmAb64 fab light chain


Mass: 23353.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody HmAb64 fab heavy chain


Mass: 24023.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 30% PEG1500, 8%MPD, 0.1M Tris pH8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→45.63 Å / Num. obs: 21339 / % possible obs: 99.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 48.4 Å2 / CC1/2: 0.995 / Net I/σ(I): 11.6
Reflection shellResolution: 2.8→2.97 Å / Mean I/σ(I) obs: 2.84 / Num. unique obs: 1621 / CC1/2: 0.882 / Rrim(I) all: 0.53

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Processing

Software
NameVersionClassification
XDS1.16_3549data processing
XDS1.16_3549data scaling
XDSdata reduction
PHENIXphasing
PHENIX1.16_3549refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DEE

1dee


Resolution: 2.8→45.63 Å / SU ML: 0.4188 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.074
RfactorNum. reflection% reflection
Rfree0.2627 978 5.01 %
Rwork0.1782 --
obs0.1822 19529 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.61 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 2 32 3342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00773384
X-RAY DIFFRACTIONf_angle_d0.9744610
X-RAY DIFFRACTIONf_chiral_restr0.0526528
X-RAY DIFFRACTIONf_plane_restr0.0101585
X-RAY DIFFRACTIONf_dihedral_angle_d16.31172031
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.950.35231410.25422664X-RAY DIFFRACTION99.89
2.95-3.130.3621370.23612650X-RAY DIFFRACTION99.71
3.13-3.370.26861410.21132642X-RAY DIFFRACTION99.89
3.37-3.710.2641400.17562664X-RAY DIFFRACTION99.82
3.71-4.250.26551380.15872650X-RAY DIFFRACTION99.93
4.25-5.350.20151390.13532641X-RAY DIFFRACTION100
5.35-45.630.25951420.18042640X-RAY DIFFRACTION99.57

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