[English] 日本語
Yorodumi
- PDB-1coa: THE EFFECT OF CAVITY CREATING MUTATIONS IN THE HYDROPHOBIC CORE O... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1coa
TitleTHE EFFECT OF CAVITY CREATING MUTATIONS IN THE HYDROPHOBIC CORE OF CHYMOTRYPSIN INHIBITOR 2
ComponentsCHYMOTRYPSIN INHIBITOR 2
KeywordsSERINE PROTEASE INHIBITOR
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / response to wounding
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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Subtilisin-chymotrypsin inhibitor-2A
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsJackson, S.E. / Moracci, M. / Elmasry, N. / Johnson, C.M. / Fersht, A.R.
Citation
Journal: Biochemistry / Year: 1993
Title: Effect of cavity-creating mutations in the hydrophobic core of chymotrypsin inhibitor 2.
Authors: Jackson, S.E. / Moracci, M. / elMasry, N. / Johnson, C.M. / Fersht, A.R.
#1: Journal: Biochemistry / Year: 1987
Title: Crystal and Molecular Structure of the Serine Proteinase Inhibitor Ci-2 from Barley Seeds
Authors: Mcphalen, C.A. / James, M.N.G.
History
DepositionMay 14, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: 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: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
I: CHYMOTRYPSIN INHIBITOR 2


Theoretical massNumber of molelcules
Total (without water)7,3011
Polymers7,3011
Non-polymers00
Water57632
1
I: CHYMOTRYPSIN INHIBITOR 2
x 12


Theoretical massNumber of molelcules
Total (without water)87,60712
Polymers87,60712
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
crystal symmetry operation9_555-x,-x+y,-z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation10_555-y,-x,-z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation11_555-x+y,y,-z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation12_555x,x-y,-z1
Unit cell
Length a, b, c (Å)68.925, 68.925, 53.094
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11I-114-

HOH

21I-115-

HOH

-
Components

#1: Protein CHYMOTRYPSIN INHIBITOR 2


Mass: 7300.581 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley) / References: UniProt: P01053
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ICI2_HORVU SWISS-PROT RESIDUE PDB ATOM RECORDS NAME NUMBER NAME CHAIN SEQ/INSERT CODE LEU 20 MET 20 GLN 78 GLU 78

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.64 %
Crystal grow
*PLUS
Temperature: 4-6 ℃ / pH: 8 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
140 %(w/v)ammonium sulfate1dropprecipitant
250 mMTris-HCl1reservoir

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 35386 / % possible obs: 95.4 % / Rmerge(I) obs: 0.107 / Biso Wilson estimate: 24.19 Å2
Reflection shell
*PLUS
Highest resolution: 2.2 Å / % possible obs: 95.2 %

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.2→13.7 Å / σ(F): 0 /
RfactorNum. reflection
obs0.171 35386
Refinement stepCycle: LAST / Resolution: 2.2→13.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms512 0 0 32 544
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.202
X-RAY DIFFRACTIONp_angle_d0.0580.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0660.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.2281.5
X-RAY DIFFRACTIONp_mcangle_it1.9642
X-RAY DIFFRACTIONp_scbond_it2.9382
X-RAY DIFFRACTIONp_scangle_it4.6283
X-RAY DIFFRACTIONp_plane_restr0.0160.02
X-RAY DIFFRACTIONp_chiral_restr0.1520.12
X-RAY DIFFRACTIONp_singtor_nbd0.1740.2
X-RAY DIFFRACTIONp_multtor_nbd0.1680.2
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1760.2
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.1683
X-RAY DIFFRACTIONp_staggered_tor16.35820
X-RAY DIFFRACTIONp_orthonormal_tor15.62115
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Num. reflection all: 35386 / Rfactor all: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20.1 Å2

+
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