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- PDB-2adg: Crystal structure of monoclonal anti-CD4 antibody Q425 -

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Basic information

Entry
Database: PDB / ID: 2adg
TitleCrystal structure of monoclonal anti-CD4 antibody Q425
Components
  • Q425 Fab Light chain
  • Q425 Fab heavy chain
KeywordsIMMUNE SYSTEM / anti-CD4 / interfacial metal / antibody recognition
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhou, T. / Hamer, D.H. / Hendrickson, W.A. / Sattentau, Q.J. / Kwong, P.D.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Interfacial metal and antibody recognition.
Authors: Zhou, T. / Hamer, D.H. / Hendrickson, W.A. / Sattentau, Q.J. / Kwong, P.D.
History
DepositionJul 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 23, 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 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE The sequence of FAB protein is not available at GB or SWS sequence database at the time of ...SEQUENCE The sequence of FAB protein is not available at GB or SWS sequence database at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Q425 Fab Light chain
B: Q425 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)47,6512
Polymers47,6512
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-27 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.715, 97.715, 112.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsHeterodimer of heavy and light chain

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Components

#1: Antibody Q425 Fab Light chain


Mass: 23721.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Hybridoma / Source: (natural) Mus musculus (house mouse)
#2: Antibody Q425 Fab heavy chain


Mass: 23929.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Hybridoma / Source: (natural) Mus musculus (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.737 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG4000, Sodium Acetate, EDTA, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jan 20, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→10 Å / Num. all: 18319 / Num. obs: 18319 / % possible obs: 94.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 15.1 Å2 / Rsym value: 0.098 / Net I/σ(I): 7.3
Reflection shellResolution: 2.5→2.61 Å / % possible all: 78.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
XUONG-HAMLIN(DETECTOR SYSTEM)data reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1FVD

1fvd


Resolution: 2.5→10 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 62726.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 894 4.9 %RANDOM
Rwork0.203 ---
all0.244 18319 --
obs0.203 18319 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.361 Å2 / ksol: 0.316614 e/Å3
Displacement parametersBiso mean: 31 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2--0.52 Å20 Å2
3----1.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3264 0 0 67 3331
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d27.5
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it2.192
X-RAY DIFFRACTIONc_scbond_it1.682
X-RAY DIFFRACTIONc_scangle_it2.72.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.335 127 4.7 %
Rwork0.337 2562 -
obs--84.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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