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- PDB-3gk8: X-ray crystal structure of the Fab from MAb 14, mouse antibody ag... -

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Basic information

Entry
Database: PDB / ID: 3gk8
TitleX-ray crystal structure of the Fab from MAb 14, mouse antibody against Canine Parvovirus
Components
  • Fab 14 Heavy ChainFragment antigen-binding
  • Fab 14 Light ChainFragment antigen-binding
KeywordsIMMUNE SYSTEM / antibody fragment from neutralizing monoclonal antibody against canine parvovirus
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsHafenstein, S. / Bowman, V. / Sun, T. / Nelson, C. / Palermo, L. / Chipman, P. / Battisti, A. / Parrish, C.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 25, 2013Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab 14 Light Chain
H: Fab 14 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)46,6112
Polymers46,6112
Non-polymers00
Water2,036113
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-25 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)168.604, 39.885, 70.745
Angle α, β, γ (deg.)90.000, 94.579, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Fab 14 Light Chain / Fragment antigen-binding


Mass: 23261.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): Hybridoma
#2: Antibody Fab 14 Heavy Chain / Fragment antigen-binding


Mass: 23349.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): Hybridoma
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.54 Å3/Da / Density % sol: 51.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 5000, 0.1M HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1 Å
DetectorDate: May 2, 2005
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 3.6 % / Av σ(I) over netI: 25.82 / Number: 147415 / Rmerge(I) obs: 0.061 / Χ2: 1.39 / D res high: 1.85 Å / D res low: 50 Å / Num. obs: 40514 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)Diffraction-IDRmerge(I) obsChi squaredRedundancy
3.995098.310.0211.3933.5
3.163.9910010.0271.3963.7
2.763.1699.910.051.3393.7
2.512.7610010.0891.3483.7
2.332.5199.910.141.3853.7
2.192.3310010.21.4063.7
2.082.1999.910.2571.3953.6
1.992.0899.910.3621.3843.6
1.921.9910010.5341.4273.7
1.851.9210010.9021.4193.6
ReflectionResolution: 1.85→50 Å / Num. obs: 40514 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.061 / Χ2: 1.389 / Net I/σ(I): 25.819
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.923.60.90240351.4191100
1.92-1.993.70.53440261.4271100
1.99-2.083.60.36240161.384199.9
2.08-2.193.60.25740241.395199.9
2.19-2.333.70.240221.4061100
2.33-2.513.70.1440301.385199.9
2.51-2.763.70.08940431.3481100
2.76-3.163.70.0540601.339199.9
3.16-3.993.70.02741281.3961100
3.99-503.50.02141301.393198.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.447 / Cor.coef. Fo:Fc: 0.449
Highest resolutionLowest resolution
Translation4 Å8 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→42.02 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.756
RfactorNum. reflection
Rfree0.306 934
Rwork0.266 -
Obs-30479
Displacement parametersBiso max: 99.13 Å2 / Biso mean: 41.161 Å2 / Biso min: 1.89 Å2
Baniso -1Baniso -2Baniso -3
1--3.358 Å20 Å26.723 Å2
2---0.676 Å20 Å2
3---4.035 Å2
Refinement stepCycle: LAST / Resolution: 2→42.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3283 0 0 113 3396
Refine LS restraints
Refinement-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.39
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.212
X-RAY DIFFRACTIONc_scbond_it1.952
X-RAY DIFFRACTIONc_scangle_it2.732.5

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