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- PDB-3v0v: Fab WN1 222-5 unliganded -

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Basic information

Entry
Database: PDB / ID: 3v0v
TitleFab WN1 222-5 unliganded
Components
  • WN1 222-5 Fab (IgG2a) heavy chain
  • WN1 222-5 Fab (IgG2a) light chain
KeywordsIMMUNE SYSTEM / Beta sheets / Antibody / Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsGomery, K. / Evans, S.V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Antibody WN1 222-5 mimics Toll-like receptor 4 binding in the recognition of LPS.
Authors: Gomery, K. / Muller-Loennies, S. / Brooks, C.L. / Brade, L. / Kosma, P. / Di Padova, F. / Brade, H. / Evans, S.V.
History
DepositionDec 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: WN1 222-5 Fab (IgG2a) light chain
H: WN1 222-5 Fab (IgG2a) heavy chain
B: WN1 222-5 Fab (IgG2a) light chain
A: WN1 222-5 Fab (IgG2a) heavy chain


Theoretical massNumber of molelcules
Total (without water)93,6164
Polymers93,6164
Non-polymers00
Water9,062503
1
L: WN1 222-5 Fab (IgG2a) light chain
H: WN1 222-5 Fab (IgG2a) heavy chain


Theoretical massNumber of molelcules
Total (without water)46,8082
Polymers46,8082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-26 kcal/mol
Surface area19180 Å2
MethodPISA
2
B: WN1 222-5 Fab (IgG2a) light chain
A: WN1 222-5 Fab (IgG2a) heavy chain


Theoretical massNumber of molelcules
Total (without water)46,8082
Polymers46,8082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-24 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.886, 48.201, 140.131
Angle α, β, γ (deg.)90.000, 110.550, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody WN1 222-5 Fab (IgG2a) light chain


Mass: 23281.783 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: NZB
#2: Antibody WN1 222-5 Fab (IgG2a) heavy chain


Mass: 23526.303 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: NZB
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 503 / 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: 2.28 Å3/Da / Density % sol: 46.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: HEPES, PEG 3350, Propanol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jun 29, 2009 / Details: Osmic blue mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.13→19.985 Å / % possible obs: 93.6 % / Redundancy: 3.18 % / Rmerge(I) obs: 0.062 / Χ2: 0.95 / Net I/σ(I): 13.1 / Scaling rejects: 545
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.7-2.83.120.223.962711999185
2.8-2.913.090.1645.2632520291.0183.9
2.91-3.043.020.1356.6632520761.0686.4
3.04-3.23.010.1087.8650621430.9790.2
3.2-3.42.990.0859.5686022840.8694
3.4-3.663.050.06712.6720223560.8597.9
3.66-4.033.230.06414.3783824130.8699
4.03-4.63.370.05318.3813923930.8999.4
4.6-5.773.450.05120.8844524300.9699.4
5.77-19.893.390.04423.9870725371.0499.9

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
CrystalCleardata reduction
d*TREKdata scaling
PHASERphasing
d*TREK9.7 W8RSSIdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YEF

1yef


Resolution: 2.13→19.985 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.97 / σ(F): 1.34 / Phase error: 30.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2843 2257 5.12 %
Rwork0.2378 --
obs0.2402 44060 92.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.885 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso max: 88.24 Å2 / Biso mean: 41.725 Å2 / Biso min: 22.18 Å2
Baniso -1Baniso -2Baniso -3
1-4.2044 Å2-0 Å20.4131 Å2
2---4.4839 Å20 Å2
3---0.2795 Å2
Refinement stepCycle: LAST / Resolution: 2.13→19.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6519 0 0 503 7022
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_deg0.733

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