[English] 日本語
Yorodumi
- PDB-1acb: CRYSTAL AND MOLECULAR STRUCTURE OF THE BOVINE ALPHA-CHYMOTRYPSIN-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1acb
TitleCRYSTAL AND MOLECULAR STRUCTURE OF THE BOVINE ALPHA-CHYMOTRYPSIN-EGLIN C COMPLEX AT 2.0 ANGSTROMS RESOLUTION
Components
  • ALPHA-CHYMOTRYPSINChymotrypsin
  • Eglin C
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


chymotrypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / response to wounding / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Trypsin Inhibitor V, subunit A / Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / Trypsin Inhibitor V; Chain A / 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. ...Trypsin Inhibitor V, subunit A / Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / Trypsin Inhibitor V; Chain A / 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 / Eglin C
Similarity search - Component
Biological speciesBos taurus (cattle)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsBolognesi, M. / Frigerio, F. / Coda, A. / Pugliese, L. / Lionetti, C. / Menegatti, E. / Amiconi, G. / Schnebli, H.P. / Ascenzi, P.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Crystal and molecular structure of the bovine alpha-chymotrypsin-eglin c complex at 2.0 A resolution.
Authors: Frigerio, F. / Coda, A. / Pugliese, L. / Lionetti, C. / Menegatti, E. / Amiconi, G. / Schnebli, H.P. / Ascenzi, P. / Bolognesi, M.
#1: Journal: J.Mol.Recog. / Year: 1990
Title: X-Ray Crystal Structure of the Bovine Alpha-Chymotrypsin(Slash)Eglin C Complex at 2.6 Angstroms Resolution
Authors: Bolognesi, M. / Pugliese, L. / Gatti, G. / Frigerio, F. / Coda, A. / Antolini, L. / Schnebli, H.P. / Menegatti, E. / Amiconi, G. / Ascenzi, P.
#2: Journal: J.Mol.Biol. / Year: 1989
Title: Preliminary Crystallographic Data on the Complex of Bovine Alpha-Chymotrypsin with the Recombinant Proteinase Inhibitor Eglin C from Hirudo Medicinalis
Authors: Pugliese, L. / Gatti, G. / Bolognesi, M. / Coda, A. / Menegatti, E. / Schnebli, H.P. / Ascenzi, P. / Amiconi, G.
History
DepositionNov 8, 1991Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Remark 700SHEET THE SHEETS PRESENTED AS *CH1* AND *CH2* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA- ...SHEET THE SHEETS PRESENTED AS *CH1* AND *CH2* 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: ALPHA-CHYMOTRYPSIN
I: Eglin C


Theoretical massNumber of molelcules
Total (without water)33,7862
Polymers33,7862
Non-polymers00
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-12 kcal/mol
Surface area13180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.300, 59.400, 42.500
Angle α, β, γ (deg.)90.00, 99.10, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES WITH POOR ELECTRON DENSITY: SER E 77, GLU E 78, ARG E 145, ALA E 149, ASN E 150, ARG E 154, GLN E 239, LYS I 8, HIS I 28, TYR I 49, ASN I 50.

-
Components

#1: Protein ALPHA-CHYMOTRYPSIN / Chymotrypsin


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, chymotrypsin
#2: Protein Eglin C


Mass: 8100.011 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hirudo medicinalis (medicinal leech) / References: UniProt: P01051
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Compound detailsEGLIN C IS BOUND NON-COVALENTLY TO THE ACTIVE SITE OF THE ENZYME.
Sequence detailsRESIDUES THR I 1, GLU I 2, PHE I 3, GLY I 4, SER I 5, GLU I 6, AND LEU I 7 OF EGLIN C HAVE BEEN ...RESIDUES THR I 1, GLU I 2, PHE I 3, GLY I 4, SER I 5, GLU I 6, AND LEU I 7 OF EGLIN C HAVE BEEN PROTEOLYTICALLY CLEAVED BY THE ENZYME DURING CRYSTALLIZATION.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.68 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, sitting drop / Details: referred to J.Mol.Biol. 208.511-513
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlalpha chymotrypsin1drop
27 mg/mleglin c1drop
30.05 Mphosphate1drop
45 %(w/v)PEG40001dropcan be replaced with PEG6000
510 %PEG40001reservoircan be replaced with PEG6000

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 11 Å / Num. obs: 16841 / Observed criterion σ(I): 5 / Num. measured all: 31318 / Rmerge(I) obs: 0.04

-
Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2→11 Å / Rfactor obs: 0.167 / σ(F): 0
Refinement stepCycle: LAST / Resolution: 2→11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2289 0 0 142 2431
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_angle_deg2.97
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.018
X-RAY DIFFRACTIONt_gen_planes0.019
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.086
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 11 Å / Num. reflection all: 16833 / σ(F): 0 / Rfactor all: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_plane_restr0.019

+
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