[English] 日本語
Yorodumi
- PDB-1ds3: CRYSTAL STRUCTURE OF OMTKY3-CH2-ASP19I -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ds3
TitleCRYSTAL STRUCTURE OF OMTKY3-CH2-ASP19I
ComponentsOVOMUCOID
KeywordsHYDROLASE INHIBITOR / canonical protein inhibitor / ovomucoid / reduced peptide bond / OMTKY3
Function / homology
Function and homology information


molecular function inhibitor activity / serine-type endopeptidase inhibitor activity / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMeleagris gallopavo (turkey)
MethodX-RAY DIFFRACTION / Resolution: 1.65 Å
AuthorsBateman, K.S. / Huang, K. / Anderson, S. / Lu, W. / Qasim, M.A. / Laskowski Jr., M. / James, M.N.G.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Contribution of peptide bonds to inhibitor-protease binding: crystal structures of the turkey ovomucoid third domain backbone variants OMTKY3-Pro18I and OMTKY3-psi[COO]-Leu18I in complex with ...Title: Contribution of peptide bonds to inhibitor-protease binding: crystal structures of the turkey ovomucoid third domain backbone variants OMTKY3-Pro18I and OMTKY3-psi[COO]-Leu18I in complex with Streptomyces griseus proteinase B (SGPB) and the structure of the free inhibitor, OMTKY-3-psi[CH2NH2+]-Asp19I
Authors: Bateman, K.S. / Huang, K. / Anderson, S. / Lu, W. / Qasim, M.A. / Laskowski Jr., M. / James, M.N.
History
DepositionJan 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 17, 2011Group: Non-polymer description
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
I: OVOMUCOID


Theoretical massNumber of molelcules
Total (without water)5,5571
Polymers5,5571
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)23.152, 36.092, 26.135
Angle α, β, γ (deg.)90.00, 97.51, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein OVOMUCOID


Mass: 5557.278 Da / Num. of mol.: 1 / Fragment: THIRD DOMAIN (OMTKY3) / Mutation: REDUCED PEPTIDE BOND BETWEEN LEU18I(2LU)-ASP19I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meleagris gallopavo (turkey)
Description: THE PEPTIDE BOND BETWEEN LEU18I(2LU) AND ASP19I HAS BEEN REDUCED.
Production host: Escherichia coli (E. coli) / References: UniProt: P68390
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 37.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: ammonium sulphate, no buffer, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Details: used seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
22.0 Mammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5417
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Apr 18, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. obs: 16933 / % possible obs: 92.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 10.64
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 0.245 / % possible all: 47.6
Reflection
*PLUS
Num. obs: 4800 / Num. measured all: 16933
Reflection shell
*PLUS
% possible obs: 47.6 %

-
Processing

Software
NameVersionClassification
XPRESSdata collection
SCALEPACKdata scaling
AMoREphasing
TNT5Erefinement
XPRESSdata reduction
RefinementResolution: 1.65→20 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.23 -Random. 5%
Rwork0.196 --
obs-4800 -
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms385 0 0 41 426
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg1.115
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_plane_restr / Dev ideal: 0.011

+
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