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- PDB-4r97: Crystal structure of the Fab fragment of KKO -

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Basic information

Entry
Database: PDB / ID: 4r97
TitleCrystal structure of the Fab fragment of KKO
Components
  • platelet factor 4 antibody KKO heavy chain
  • platelet factor 4 antibody KKO light chain
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCai, Z. / Zhu, Z. / Liu, Q. / Greene, M.I.
CitationJournal: Nat Commun / Year: 2015
Title: Atomic description of the immune complex involved in heparin-induced thrombocytopenia.
Authors: Cai, Z. / Yarovoi, S.V. / Zhu, Z. / Rauova, L. / Hayes, V. / Lebedeva, T. / Liu, Q. / Poncz, M. / Arepally, G. / Cines, D.B. / Greene, M.I.
History
DepositionSep 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: platelet factor 4 antibody KKO light chain
C: platelet factor 4 antibody KKO heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6339
Polymers47,0422
Non-polymers5917
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-87 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.482, 92.124, 122.144
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody platelet factor 4 antibody KKO light chain


Mass: 23725.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): HYBRIDOMA / Production host: Mus musculus (house mouse)
#2: Antibody platelet factor 4 antibody KKO heavy chain


Mass: 23316.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): HYBRIDOMA / Production host: Mus musculus (house mouse)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.48 Å3/Da / Density % sol: 50.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 14% PEG2000, 0.06M zinc acetate, 0.1M sodium cacodylate pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 1, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 24599 / Num. obs: 23211 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.088
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.2-2.284.90.6612.22358198.5
2.28-2.374.90.5412.672359198.2
2.37-2.484.90.4593.272386198.4
2.48-2.6150.3414.742363197.7
2.61-2.7750.2416.962367197.2
2.77-2.995.10.16711.452349196.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30.825 Å / SU ML: 0.32 / σ(F): 0 / Phase error: 28.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2617 1191 5.15 %RANDOM
Rwork0.1998 ---
all0.203 24599 --
obs0.203 23127 94.15 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→30.825 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3286 0 32 99 3417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083401
X-RAY DIFFRACTIONf_angle_d1.1694624
X-RAY DIFFRACTIONf_dihedral_angle_d14.8991199
X-RAY DIFFRACTIONf_chiral_restr0.08519
X-RAY DIFFRACTIONf_plane_restr0.005589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.28720.32481500.27612425X-RAY DIFFRACTION97
2.2872-2.39130.311340.2422502X-RAY DIFFRACTION98
2.3913-2.51730.31591180.22182499X-RAY DIFFRACTION98
2.5173-2.67490.2911430.22222475X-RAY DIFFRACTION97
2.6749-2.88130.31251280.23262493X-RAY DIFFRACTION96
2.8813-3.1710.3271270.22782484X-RAY DIFFRACTION96
3.171-3.62930.28471410.19782395X-RAY DIFFRACTION94
3.6293-4.57010.19261330.17172299X-RAY DIFFRACTION88
4.5701-30.82760.23691170.17932364X-RAY DIFFRACTION85

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