[English] 日本語
Yorodumi
- PDB-1cgi: THREE-DIMENSIONAL STRUCTURE OF THE COMPLEXES BETWEEN BOVINE CHYMO... -

+
Open data


ID or keywords:

Loading...

-
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 / response to nutrient levels / positive regulation of epithelial cell proliferation / 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 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 / 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
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.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more