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- PDB-1cr9: CRYSTAL STRUCTURE OF THE ANTI-PRION FAB 3F4 -

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Basic information

Entry
Database: PDB / ID: 1cr9
TitleCRYSTAL STRUCTURE OF THE ANTI-PRION FAB 3F4
Components
  • FAB ANTIBODY HEAVY CHAIN
  • FAB ANTIBODY LIGHT CHAIN
KeywordsIMMUNE SYSTEM / anti-prion antibody / Fab 3F4
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsKanyo, Z.F. / Pan, K.M. / Williamson, R.A. / Burton, D.R. / Prusiner, S.B. / Fletterick, R.J. / Cohen, F.E.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Antibody binding defines a structure for an epitope that participates in the PrPC-->PrPSc conformational change.
Authors: Kanyo, Z.F. / Pan, K.M. / Williamson, R.A. / Burton, D.R. / Prusiner, S.B. / Fletterick, R.J. / Cohen, F.E.
History
DepositionAug 14, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: FAB ANTIBODY LIGHT CHAIN
H: FAB ANTIBODY HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)47,4242
Polymers47,4242
Non-polymers00
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-24 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.900, 77.600, 70.600
Angle α, β, γ (deg.)90.00, 110.56, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Antibody FAB ANTIBODY LIGHT CHAIN / ANTI-PRION FAB 3F4


Mass: 24080.775 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody FAB ANTIBODY HEAVY CHAIN / ANTI-PRION FAB 3F4


Mass: 23342.943 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulphate, PEG 400, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMMOPS1drop
220 mg/mlprotein1drop
350 mM1dropNaCl
42 mM1dropNaN3
52.0 Mammonium sulfate1reservoir
62 %(v/v)PEG4001reservoir
7100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 30, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 33314 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.22 / Num. unique all: 2242 / % possible all: 90.6
Reflection
*PLUS
Num. obs: 33314
Reflection shell
*PLUS
% possible obs: 90.6 % / Num. unique obs: 2242 / Rmerge(I) obs: 0.22

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Processing

Software
NameVersionClassification
SCALAdata scaling
AMoREphasing
X-PLOR3.1refinement
CCP4(SCALA)data scaling
RefinementResolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1651 5 %random
Rwork0.171 ---
all-33303 --
Solvent computationSolvent model: Bulk-solvent model used
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3334 0 0 182 3516
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.782
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS

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