[English] 日本語
Yorodumi
- PDB-8gqq: The three-dimensional structure of Cystatin A2, a cysteine protea... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gqq
TitleThe three-dimensional structure of Cystatin A2, a cysteine protease inhibitor from Dictyostelium discoideum
ComponentsCystatin-A2
KeywordsSTRUCTURAL PROTEIN / cystatin A2 / cysteine protease inhibitor / inhibition activity
Function / homologyProteinase inhibitor I25A, stefin / Neutrophil degranulation / Cystatin domain / Cystatin domain / Cystatin superfamily / regulation of proteolysis / cysteine-type endopeptidase inhibitor activity / cytosol / Cystatin-A2
Function and homology information
Biological speciesDictyostelium discoideum AX3 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.069 Å
AuthorsDinh, T.T. / Dao, O. / Lee, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: The three-dimensional structure of Cystatin A2, a cysteine protease inhibitor from Dictyostelium discoideum
Authors: Dinh, T.T. / Dao, O. / Lee, K.H.
History
DepositionAug 30, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cystatin-A2


Theoretical massNumber of molelcules
Total (without water)10,8521
Polymers10,8521
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.273, 63.274, 24.911
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-220-

HOH

-
Components

#1: Protein Cystatin-A2


Mass: 10852.265 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum AX3 (eukaryote)
Gene: cpiB, DDB_G0280439
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q65YR7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 22% (w/v) PEG 2K, 100 mM MES pH 6.5, 60 mM sodium acetate, 10 mM TCEP

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.069→24.911 Å / Num. obs: 42018 / % possible obs: 99.05 % / Redundancy: 13.5 % / Biso Wilson estimate: 9.34 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 10.8
Reflection shellResolution: 1.069→1.107 Å / Rmerge(I) obs: 0.39 / Num. unique obs: 4113

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KFQ

3kfq


Resolution: 1.069→24.911 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1899 2041 4.86 %
Rwork0.1787 39967 -
obs0.1793 42008 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 45.58 Å2 / Biso mean: 14.9737 Å2 / Biso min: 5.57 Å2
Refinement stepCycle: final / Resolution: 1.069→24.911 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms762 0 0 132 894
Biso mean---25.19 -
Num. residues----99
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.069-1.09360.20591390.2049260898
1.0936-1.12090.21951070.19142652100
1.1209-1.15120.20681430.18772640100
1.1512-1.18510.19941030.17432701100
1.1851-1.22330.18861290.18272628100
1.2233-1.26710.19381490.18212658100
1.2671-1.31780.22321360.18712682100
1.3178-1.37780.19221530.17582635100
1.3778-1.45040.18921480.1792660100
1.4504-1.54130.19681380.16652663100
1.5413-1.66020.1621470.1612697100
1.6602-1.82730.17771460.17142667100
1.8273-2.09160.17461260.16712757100
2.0916-2.63470.18721450.17192738100
Refinement TLS params.Method: refined / Origin x: 2.1566 Å / Origin y: 16.2658 Å / Origin z: 4.6508 Å
111213212223313233
T0.0624 Å2-0.0081 Å20.0039 Å2-0.0642 Å2-0.0026 Å2--0.0315 Å2
L2.131 °20.0597 °20.0672 °2-1.7902 °20.0098 °2--1.8207 °2
S-0.0469 Å °-0.0274 Å °-0.0421 Å °-0.0288 Å °0.0124 Å °-0.0075 Å °0.038 Å °0.0716 Å °0.0287 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-3 - 95
2X-RAY DIFFRACTION1allW1 - 141

+
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