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- PDB-5uby: Fab structure of anti-HIV-1 gp120 mAb 1A8 -

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Basic information

Entry
Database: PDB / ID: 5uby
TitleFab structure of anti-HIV-1 gp120 mAb 1A8
Components
  • Heavy chain of Fab fragment of anti-HIV1 gp120 mAb 1A8
  • Light chain of Fab fragment of anti-HIV1 gp120 mAb 1A8
KeywordsIMMUNE SYSTEM / HIV / gp120 / Antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPan, R. / Kong, X.-P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI58706 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI100151 United States
CitationJournal: To be Published
Title: High Antibody Diversity and Low Inter-clonal Competition Favor Production of Functional Neutralizing Antibodies
Authors: Smith, S.A. / Burton, S.L. / Spicer, L. / Pan, R. / Kilembe, W. / Lakhi, S. / Karita, E. / Price, M. / Allen, S. / Hunter, E. / Kong, X.-P. / Derdeyn, C.A.
History
DepositionDec 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Heavy chain of Fab fragment of anti-HIV1 gp120 mAb 1A8
L: Light chain of Fab fragment of anti-HIV1 gp120 mAb 1A8


Theoretical massNumber of molelcules
Total (without water)46,7092
Polymers46,7092
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-24 kcal/mol
Surface area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.098, 40.121, 77.195
Angle α, β, γ (deg.)90.00, 104.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Heavy chain of Fab fragment of anti-HIV1 gp120 mAb 1A8


Mass: 24285.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mammalia (mammals)
#2: Antibody Light chain of Fab fragment of anti-HIV1 gp120 mAb 1A8


Mass: 22423.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mammalia (mammals)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18% (w/v) polyethylene glycol (PEG) 8000, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.6→44.74 Å / Num. obs: 24889 / % possible obs: 99.7 % / Redundancy: 4.15 % / CC1/2: 0.999 / Net I/σ(I): 19.87
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 4.18 % / Mean I/σ(I) obs: 2.16 / CC1/2: 0.736 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
PHENIXmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FQQ

4fqq


Resolution: 2.6→44.736 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.54
RfactorNum. reflection% reflection
Rfree0.2486 1260 5.06 %
Rwork0.1876 --
obs0.1907 24889 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→44.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3287 0 0 37 3324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093377
X-RAY DIFFRACTIONf_angle_d1.1244614
X-RAY DIFFRACTIONf_dihedral_angle_d15.9552002
X-RAY DIFFRACTIONf_chiral_restr0.058521
X-RAY DIFFRACTIONf_plane_restr0.007585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6004-2.70450.37391430.34032638X-RAY DIFFRACTION99
2.7045-2.82760.45281380.3152571X-RAY DIFFRACTION100
2.8276-2.97660.34851380.26652655X-RAY DIFFRACTION100
2.9766-3.16310.3371340.25352602X-RAY DIFFRACTION100
3.1631-3.40720.27431410.23662657X-RAY DIFFRACTION100
3.4072-3.74990.30581430.18812610X-RAY DIFFRACTION100
3.7499-4.29220.20581450.16522654X-RAY DIFFRACTION100
4.2922-5.40620.1991400.13562626X-RAY DIFFRACTION100
5.4062-44.7430.17741380.14552616X-RAY DIFFRACTION99

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