[English] 日本語
Yorodumi
- PDB-1gmd: X-ray crystal structure of gamma-chymotrypsin in hexane -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gmd
TitleX-ray crystal structure of gamma-chymotrypsin in hexane
Components
  • (GAMMA-CHYMOTRYPSIN ...) x 3
  • PRO GLY ALA TYR ASP PEPTIDE
KeywordsHYDROLASE / SERINE PROTEASE
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
HEXANE / Chymotrypsinogen A
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsYennawar, N.H. / Yennawar, H.P. / Banerjee, S. / Farber, G.K.
CitationJournal: Biochemistry / Year: 1994
Title: X-ray crystal structure of gamma-chymotrypsin in hexane.
Authors: Yennawar, N.H. / Yennawar, H.P. / Farber, G.K.
History
DepositionAug 20, 1993-
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 1.3Apr 24, 2013Group: Derived calculations
Remark 700SHEET THE SHEETS PRESENTED AS *S1* AND *S2* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA ...SHEET THE SHEETS PRESENTED AS *S1* AND *S2* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA BARRELS. THIS IS REPRESENTED BY SEVEN-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: GAMMA-CHYMOTRYPSIN A
F: GAMMA-CHYMOTRYPSIN A
G: GAMMA-CHYMOTRYPSIN A
B: PRO GLY ALA TYR ASP PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,38711
Polymers25,7844
Non-polymers6037
Water2,342130
1
E: GAMMA-CHYMOTRYPSIN A
F: GAMMA-CHYMOTRYPSIN A
G: GAMMA-CHYMOTRYPSIN A
B: PRO GLY ALA TYR ASP PEPTIDE
hetero molecules

E: GAMMA-CHYMOTRYPSIN A
F: GAMMA-CHYMOTRYPSIN A
G: GAMMA-CHYMOTRYPSIN A
B: PRO GLY ALA TYR ASP PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,77522
Polymers51,5688
Non-polymers1,20614
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
Unit cell
Length a, b, c (Å)69.340, 69.320, 97.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

-
Components

-
GAMMA-CHYMOTRYPSIN ... , 3 types, 3 molecules EFG

#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

-
Protein/peptide , 1 types, 1 molecules B

#4: Protein/peptide PRO GLY ALA TYR ASP PEPTIDE


Mass: 521.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)

-
Non-polymers , 2 types, 137 molecules

#5: Chemical
ChemComp-HEX / HEXANE / Hexane


Mass: 86.175 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsRESIDUES 500 - 505 ARE A PENTAPEPTIDE IN THE ACTIVE SITE AS A TETRAHEDRAL INTERMEDIATE. C OF ...RESIDUES 500 - 505 ARE A PENTAPEPTIDE IN THE ACTIVE SITE AS A TETRAHEDRAL INTERMEDIATE. C OF RESIDUE TYR 504 IS TETRAHEDRAL AND IS COVALENTLY LINKED TO SER 195 OG AND N OF ASP 505. THE CARBOXY TERMINUS OF ASP 505 WAS NOT CLEAR IN THE ELECTRON DENSITY MAP AND HAS NOT BEEN MODELLED.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.85 %
Crystal grow
*PLUS
pH: 5.6 / Method: batch method
Details: referred to 'Stoddard, B. L.', (1990) Biochemistry, 29, 4871-4879
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlchymotrypsin11
210 mMsodium cacodylate11
30.75 %satcetyltrimethylammonium bromide11
445 %satammonium sulfate11
565 %satammonium sulphate12

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.2 Å
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 7606 / Observed criterion σ(I): 2 / Num. measured all: 13982 / Rmerge(I) obs: 0.092

-
Processing

SoftwareName: X-PLOR / Version: 1GMD / Classification: refinement
RefinementRfactor Rwork: 0.176 / Rfactor obs: 0.176 / Highest resolution: 2.2 Å
Refinement stepCycle: LAST / Highest resolution: 2.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1772 0 42 130 1944
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.82
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 5 Å / Rfactor obs: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.82

+
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://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