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- PDB-1cgi: THREE-DIMENSIONAL STRUCTURE OF THE COMPLEXES BETWEEN BOVINE CHYMO... -

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Basic information

Entry
Database: PDB / ID: 1cgi
TitleTHREE-DIMENSIONAL STRUCTURE OF THE COMPLEXES BETWEEN BOVINE CHYMOTRYPSINOGEN*A AND TWO RECOMBINANT VARIANTS OF HUMAN PANCREATIC SECRETORY TRYPSIN INHIBITOR (KAZAL-TYPE)
Components
  • ALPHA-CHYMOTRYPSINOGEN
  • PANCREATIC SECRETORY TRYPSIN INHIBITOR (KAZAL TYPE) VARIANT 3
KeywordsSERINE PROTEASE/INHIBITOR COMPLEX / SERINE PROTEASE-INHIBITOR COMPLEX / SERINE PROTEASE-INHIBITOR COMPLEX complex
Function / homology
Function and homology information


negative regulation of nitric oxide mediated signal transduction / regulation of acrosome reaction / positive regulation of pancreatic juice secretion / regulation of store-operated calcium entry / negative regulation of peptidyl-tyrosine phosphorylation / chymotrypsin / negative regulation of calcium ion import / cellular response to peptide hormone stimulus / sperm capacitation / endopeptidase inhibitor activity ...negative regulation of nitric oxide mediated signal transduction / regulation of acrosome reaction / positive regulation of pancreatic juice secretion / regulation of store-operated calcium entry / negative regulation of peptidyl-tyrosine phosphorylation / chymotrypsin / negative regulation of calcium ion import / cellular response to peptide hormone stimulus / sperm capacitation / endopeptidase inhibitor activity / positive regulation of peptide hormone secretion / serpin family protein binding / nitric oxide mediated signal transduction / serine protease inhibitor complex / digestion / positive regulation of epithelial cell proliferation / response to nutrient levels / serine-type endopeptidase inhibitor activity / positive regulation of cytosolic calcium ion concentration / response to ethanol / serine-type endopeptidase activity / proteolysis / extracellular exosome / extracellular region
Similarity search - Function
Proteinase inhibitor I1, Kazal-type, metazoa / Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Serine proteases, trypsin family, histidine active site ...Proteinase inhibitor I1, Kazal-type, metazoa / Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 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 family, serine active site. / Serine proteases, trypsin domain profile. / 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 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chymotrypsinogen A / Serine protease inhibitor Kazal-type 1
Similarity search - Component
Biological speciesBos taurus (cattle)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsHecht, H.J. / Szardenings, M. / Collins, J. / Schomburg, D.
CitationJournal: J.Mol.Biol. / Year: 1991
Title: Three-dimensional structure of the complexes between bovine chymotrypsinogen A and two recombinant variants of human pancreatic secretory trypsin inhibitor (Kazal-type).
Authors: Hecht, H.J. / Szardenings, M. / Collins, J. / Schomburg, D.
History
DepositionOct 8, 1991Processing site: BNL
Revision 1.0Oct 31, 1993Provider: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700SHEET THE SHEETS PRESENTED AS *AA* AND *BA* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA ...SHEET THE SHEETS PRESENTED AS *AA* AND *BA* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA BARRELS. THESE ARE REPRESENTED AS SEVEN-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: ALPHA-CHYMOTRYPSINOGEN
I: PANCREATIC SECRETORY TRYPSIN INHIBITOR (KAZAL TYPE) VARIANT 3


Theoretical massNumber of molelcules
Total (without water)32,0332
Polymers32,0332
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-14 kcal/mol
Surface area12590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.400, 84.400, 86.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein ALPHA-CHYMOTRYPSINOGEN


Mass: 25686.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P00766
#2: Protein PANCREATIC SECRETORY TRYPSIN INHIBITOR (KAZAL TYPE) VARIANT 3


Mass: 6347.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00995
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.94 %
Crystal grow
*PLUS
pH: 8.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
210 mg/mlinhibitor1drop
350 mMTris-HCl1drop
41.4-1.6 Mammonium sulfate1reservoir
1enzyme1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. all: 14528 / Num. obs: 10379 / % possible obs: 71.4 % / Observed criterion σ(I): 2 / Num. measured all: 27079 / Rmerge(I) obs: 0.062

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.3→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.195 10379
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2239 0 0 52 2291
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0560.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0590.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.2691
X-RAY DIFFRACTIONp_mcangle_it2.3131.5
X-RAY DIFFRACTIONp_scbond_it1.1581
X-RAY DIFFRACTIONp_scangle_it2.0881.5
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.1920.15
X-RAY DIFFRACTIONp_singtor_nbd0.2230.5
X-RAY DIFFRACTIONp_multtor_nbd0.3130.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3080.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.3123
X-RAY DIFFRACTIONp_staggered_tor24.4315
X-RAY DIFFRACTIONp_orthonormal_tor25.6520
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 8 Å / Num. reflection obs: 10379 / σ(F): 2 / Rfactor obs: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_plane_restr0.014
X-RAY DIFFRACTIONp_chiral_restr0.192

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