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- PDB-2cga: BOVINE CHYMOTRYPSINOGEN A. X-RAY CRYSTAL STRUCTURE ANALYSIS AND R... -

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Basic information

Entry
Database: PDB / ID: 2cga
TitleBOVINE CHYMOTRYPSINOGEN A. X-RAY CRYSTAL STRUCTURE ANALYSIS AND REFINEMENT OF A NEW CRYSTAL FORM AT 1.8 ANGSTROMS RESOLUTION
ComponentsCHYMOTRYPSINOGEN A
KeywordsHYDROLASE(ZYMOGEN)
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: 1.8 Å
AuthorsWang, D. / Bode, W. / Huber, R.
Citation
Journal: J.Mol.Biol. / Year: 1985
Title: Bovine chymotrypsinogen A X-ray crystal structure analysis and refinement of a new crystal form at 1.8 A resolution.
Authors: Wang, D. / Bode, W. / Huber, R.
#1: Journal: J.Mol.Biol. / Year: 1979
Title: The Transition of Bovine Trypsinogen to a Trypsin-Like State Upon Strong Ligand Binding. II. The Binding of the Pancreatic Trypsin Inhibitor and of Isoleucine-Valine and of Sequentially ...Title: The Transition of Bovine Trypsinogen to a Trypsin-Like State Upon Strong Ligand Binding. II. The Binding of the Pancreatic Trypsin Inhibitor and of Isoleucine-Valine and of Sequentially Related Peptides to Trypsinogen and to P-Guanidinobenzoate-Trypsinogen
Authors: Bode, W.
#2: Journal: J.Mol.Biol. / Year: 1977
Title: Crystal Structure of Bovine Trypsinogen at 1.8 Angstroms Resolution. II. Crystallographic Refinement, Refined Crystal Structure and Comparison with Bovine Trypsin
Authors: Fehlhammer, H. / Bode, W. / Huber, R.
#3: Journal: J.Mol.Biol. / Year: 1976
Title: Crystal Structure of Bovine Trypsinogen at 1.8 Angstroms Resolution. I. Data Collection, Application of Patterson Search Techniques and Preliminary Structural Interpretation
Authors: Bode, W. / Fehlhammer, H. / Huber, R.
#4: Journal: Biochemistry / Year: 1970
Title: Chymotrypsinogen. 2.5-Angstroms Crystal Structure, Comparison with Alpha-Chymotrypsin, and Implications for Zymogen Activation
Authors: Freer, S.T. / Kraut, J. / Robertus, J.D. / Wright, H.T. / Xuong, N.H.
History
DepositionJan 16, 1987Processing site: BNL
Revision 1.0Apr 16, 1987Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHYMOTRYPSINOGEN A
B: CHYMOTRYPSINOGEN A


Theoretical massNumber of molelcules
Total (without water)51,3722
Polymers51,3722
Non-polymers00
Water5,927329
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.300, 77.100, 110.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES VAL A 17 AND VAL B 17 HAVE UNUSUAL MAIN CHAIN CONFORMATION.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9877, 0.155, 0.0177), (0.0228, -0.0314, -0.9992), (-0.1543, 0.9874, -0.0346)
Vector: 6.217, 115.616, -3.748)
DetailsTHE TRANSFORMATION PRESENTED ON THE *MTRIX* RECORDS BELOW WILL YIELD COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*.

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Components

#1: Protein CHYMOTRYPSINOGEN A


Mass: 25686.037 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P00766
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal grow
*PLUS
pH: 4.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 %(v/v)ethanol1reservoir
20.2 Mphosphate1reservoir
32.5 mg/cm3bovine pancreatic trypsin inhibitor1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 32818 / % possible obs: 69 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.086 / Num. measured all: 87718

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Processing

SoftwareName: EREF / Classification: refinement
RefinementResolution: 1.8→6 Å /
RfactorNum. reflection
Rwork0.173 -
obs-30617
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3598 0 0 329 3927
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.016
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2.5
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 6 Å / Num. reflection obs: 30617 / Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: o_angle_d

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