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- PDB-4ztp: Fab structure of rabbit monoclonal antibody R53 targeting an epit... -

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Basic information

Entry
Database: PDB / ID: 4ztp
TitleFab structure of rabbit monoclonal antibody R53 targeting an epitope in HIV-1 gp120 C4 region
Components
  • Heavy chain of Fab fragment of rabbit monoclonal antibody R53
  • Light chain of Fab fragment of rabbit monoclonal antibody R53
KeywordsIMMUNE SYSTEM / HIV-1 / Env / C4 / CD4 / monoclonal antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsPan, R. / Kong, X.-P.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI082274 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI082676 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI065250 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI100151 United States
CitationJournal: Emerg Microbes Infect / Year: 2015
Title: Structural analysis of a novel rabbit monoclonal antibody R53 targeting an epitope in HIV-1 gp120 C4 region critical for receptor and co-receptor binding.
Authors: Pan, R. / Chen, Y. / Vaine, M. / Hu, G. / Wang, S. / Lu, S. / Kong, X.P.
History
DepositionMay 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Data collection / Derived calculations / Experimental preparation
Category: diffrn_detector / exptl_crystal_grow / pdbx_struct_oper_list
Item: _diffrn_detector.type / _exptl_crystal_grow.pH / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.classification
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _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: Light chain of Fab fragment of rabbit monoclonal antibody R53
H: Heavy chain of Fab fragment of rabbit monoclonal antibody R53


Theoretical massNumber of molelcules
Total (without water)46,3452
Polymers46,3452
Non-polymers00
Water11,241624
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-30 kcal/mol
Surface area19570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.433, 78.553, 68.480
Angle α, β, γ (deg.)90.00, 92.25, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Light chain of Fab fragment of rabbit monoclonal antibody R53


Mass: 23022.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#2: Antibody Heavy chain of Fab fragment of rabbit monoclonal antibody R53


Mass: 23322.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 624 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.77 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 14% polyethylene glycol 8000, 0.1 M HEPES pH 7.5, and 8% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0333 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0333 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 66122 / % possible obs: 95.4 % / Redundancy: 3.9 % / Rsym value: 0.056 / Net I/σ(I): 21.5
Reflection shellResolution: 1.63→1.66 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.35 / Rsym value: 0.44 / % possible all: 79

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JO1

4jo1


Resolution: 1.63→31.487 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.09 / Phase error: 24.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2277 3348 5.07 %
Rwork0.1946 --
obs0.1963 66081 94.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.63→31.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3251 0 0 624 3875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073336
X-RAY DIFFRACTIONf_angle_d1.0964564
X-RAY DIFFRACTIONf_dihedral_angle_d13.281151
X-RAY DIFFRACTIONf_chiral_restr0.043541
X-RAY DIFFRACTIONf_plane_restr0.005579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6298-1.65310.3164900.28031891X-RAY DIFFRACTION69
1.6531-1.67780.28961180.27892263X-RAY DIFFRACTION83
1.6778-1.7040.29571340.26282434X-RAY DIFFRACTION89
1.704-1.73190.31041380.27182577X-RAY DIFFRACTION94
1.7319-1.76180.29411250.26712621X-RAY DIFFRACTION96
1.7618-1.79380.30761480.2522689X-RAY DIFFRACTION97
1.7938-1.82830.26271450.24642676X-RAY DIFFRACTION97
1.8283-1.86560.28511370.22172625X-RAY DIFFRACTION97
1.8656-1.90620.23741510.21922655X-RAY DIFFRACTION97
1.9062-1.95050.27031340.21942696X-RAY DIFFRACTION98
1.9505-1.99930.22911480.20292660X-RAY DIFFRACTION97
1.9993-2.05330.24971380.20352687X-RAY DIFFRACTION97
2.0533-2.11370.22181210.20822686X-RAY DIFFRACTION98
2.1137-2.18190.2451440.21332687X-RAY DIFFRACTION98
2.1819-2.25990.25391450.21382687X-RAY DIFFRACTION98
2.2599-2.35040.24181430.20692718X-RAY DIFFRACTION98
2.3504-2.45730.24631330.21962714X-RAY DIFFRACTION98
2.4573-2.58680.24041460.21332678X-RAY DIFFRACTION98
2.5868-2.74880.27091750.20742725X-RAY DIFFRACTION98
2.7488-2.96090.27721510.20682685X-RAY DIFFRACTION99
2.9609-3.25850.21261590.18822741X-RAY DIFFRACTION99
3.2585-3.72940.19481540.16822720X-RAY DIFFRACTION99
3.7294-4.69620.18611420.15212689X-RAY DIFFRACTION96
4.6962-31.49310.19071290.17512529X-RAY DIFFRACTION89

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