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- PDB-2gch: REFINED CRYSTAL STRUCTURE OF GAMMA-CHYMOTRYPSIN AT 1.9 ANGSTROMS ... -

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Basic information

Entry
Database: PDB / ID: 2gch
TitleREFINED CRYSTAL STRUCTURE OF GAMMA-CHYMOTRYPSIN AT 1.9 ANGSTROMS RESOLUTION
Components(GAMMA-CHYMOTRYPSIN A) x 3
KeywordsHYDROLASE (SERINE PROTEINASE)
Function / homology
Function and homology information


chymotrypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsCohen, G.H. / Davies, D.R. / Silverton, E.W.
Citation
Journal: J.Mol.Biol. / Year: 1981
Title: Refined crystal structure of gamma-chymotrypsin at 1.9 A resolution. Comparison with other pancreatic serine proteases.
Authors: Cohen, G.H. / Silverton, E.W. / Davies, D.R.
#1: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1972
Title: The Stereochemistry of Substrate Binding to Chymotrypsin A Gamma
Authors: Segal, D.M. / Cohen, G.H. / Davies, D.R. / Powers, J.C. / Wilcox, P.E.
#2: Journal: Biochemistry / Year: 1971
Title: Substrate Binding Site in Chymotrypsin A Gamma, Crystallographic Study Using Peptide Chloromethyl Ketones as Site-Specific Inhibitors
Authors: Segal, D.M. / Powers, J.C. / Cohen, G.H. / Davies, D.R. / Wilcox, P.E.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1970
Title: The Relation between Gamma-and Alpha-Chymotrypsin, II.Direct Comparison of the Electron Densities at 5.5 Angstroms Resolution
Authors: Cohen, G.H. / Matthews, B.W. / Davies, D.R.
#4: Journal: J.Mol.Biol. / Year: 1969
Title: Structure of Gamma-Chymotrypsin at 5.5 Angstroms Resolution
Authors: Cohen, G.H. / Silverton, E.W. / Matthews, B.W. / Braxton, H. / Davies, D.R.
#5: Journal: J.Mol.Biol. / Year: 1968
Title: Relation between Gamma-and Alpha-Chymotrypsin
Authors: Matthews, B.W. / Cohen, G.H. / Silverton, E.W. / Braxton, H. / Davies, D.R.
#6: Journal: Proc.Natl.Acad.Sci.USA / Year: 1964
Title: The Isomorphous Heavy-Atom Substitution at the Active Site of Gamma Chymotrypsin
Authors: Sigler, P.B. / Skinner, H.C.W. / Coulter, C.L. / Kallos, J. / Braxton, H. / Davies, D.R.
#7: Journal: Atlas of Macromolecular Structure on Microfiche / Year: 1976
#8: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1972
History
DepositionMay 21, 1980-
SupersessionJul 9, 1980ID: 1GCH
Revision 1.0Jul 9, 1980Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: GAMMA-CHYMOTRYPSIN A
F: GAMMA-CHYMOTRYPSIN A
G: GAMMA-CHYMOTRYPSIN A


Theoretical massNumber of molelcules
Total (without water)25,2633
Polymers25,2633
Non-polymers00
Water2,720151
1
E: GAMMA-CHYMOTRYPSIN A
F: GAMMA-CHYMOTRYPSIN A
G: GAMMA-CHYMOTRYPSIN A

E: GAMMA-CHYMOTRYPSIN A
F: GAMMA-CHYMOTRYPSIN A
G: GAMMA-CHYMOTRYPSIN A


Theoretical massNumber of molelcules
Total (without water)50,5256
Polymers50,5256
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-57 kcal/mol
Surface area10050 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)69.600, 69.600, 97.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11F-229-

HOH

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Components

#1: Protein/peptide GAMMA-CHYMOTRYPSIN A


Mass: 1253.511 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00766, chymotrypsin
#2: Protein GAMMA-CHYMOTRYPSIN A


Mass: 13934.556 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00766, chymotrypsin
#3: Protein GAMMA-CHYMOTRYPSIN A


Mass: 10074.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00766, chymotrypsin
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal grow
*PLUS
pH: 5.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
250 %satammonium sulfate11
1protein1125mg

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. all: 19650 / Num. obs: 15395

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.9→7 Å /
RfactorNum. reflection
Rwork0.181 -
obs-14992
Refinement stepCycle: LAST / Resolution: 1.9→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1738 0 0 151 1889
Refinement
*PLUS
Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_plane_restr0.0120.02
X-RAY DIFFRACTIONo_chiral_restr0.2080.15

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