[English] 日本語
Yorodumi
- PDB-4an8: Structure of Thermus thermophilus CasA (Cse1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4an8
TitleStructure of Thermus thermophilus CasA (Cse1)
ComponentsCSE1
KeywordsIMMUNE SYSTEM / CRISPR / CASCADE / CASA
Function / homologyTopoisomerase I; Chain A, domain 4 - #100 / CRISPR-associated protein Cse1 / CRISPR-associated protein Cse1 (CRISPR_cse1) / Topoisomerase I; Chain A, domain 4 / defense response to virus / Orthogonal Bundle / Mainly Alpha / ACETATE ION / CRISPR-associated protein CasA/Cse1
Function and homology information
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsSashital, D.G. / Wiedenheft, B. / Doudna, J.A.
CitationJournal: Mol.Cell / Year: 2012
Title: Mechanism of Foreign DNA Selection in a Bacterial Adaptive Immune System.
Authors: Sashital, D.G. / Wiedenheft, B. / Doudna, J.A.
History
DepositionMar 16, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Other

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CSE1
B: CSE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,2685
Polymers113,0912
Non-polymers1773
Water6,269348
1
A: CSE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6633
Polymers56,5451
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CSE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6042
Polymers56,5451
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.360, 48.110, 129.780
Angle α, β, γ (deg.)90.00, 97.03, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein CSE1


Mass: 56545.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: TEV PROTEASE SCAR AT N-TERMINUS (GAGS) / Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Gene: TTHB188 / Plasmid: PSV272 (PET VECTOR WITH ADDED TEV PROTEASE SITE) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q53VY1
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 6.5 / Details: 2.1M NAAC, MES PH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.3→46.83 Å / Num. obs: 51896 / % possible obs: 99.6 % / Observed criterion σ(I): 2.5 / Redundancy: 3.9 % / Biso Wilson estimate: 36.16 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.9
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.9 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.3→46.825 Å / SU ML: 0.67 / σ(F): 1.99 / Phase error: 23.33 / Stereochemistry target values: ML
Details: CHAIN A RESIDUES 1-3, 130-143, 401-411 AND 497-502 ARE DISORDERED. CHAIN B RESIDUES 1-4, 129-143, 401-423 AND 494-502 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2472 2594 5 %
Rwork0.1959 --
obs0.1984 51896 99.59 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.448 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso mean: 44.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.2968 Å20 Å21.022 Å2
2--0.7999 Å20 Å2
3----1.0967 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.825 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7301 0 12 348 7661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097517
X-RAY DIFFRACTIONf_angle_d1.11910206
X-RAY DIFFRACTIONf_dihedral_angle_d14.1862842
X-RAY DIFFRACTIONf_chiral_restr0.0751102
X-RAY DIFFRACTIONf_plane_restr0.0061346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.34180.31071280.25382433X-RAY DIFFRACTION96
2.3418-2.38680.30891350.24262582X-RAY DIFFRACTION100
2.3868-2.43560.28211360.23742571X-RAY DIFFRACTION100
2.4356-2.48850.26671360.23122587X-RAY DIFFRACTION100
2.4885-2.54640.30191360.22942595X-RAY DIFFRACTION100
2.5464-2.61010.27641350.23012552X-RAY DIFFRACTION100
2.6101-2.68060.30131370.22792607X-RAY DIFFRACTION100
2.6806-2.75950.29971350.22192557X-RAY DIFFRACTION100
2.7595-2.84860.29021370.21982607X-RAY DIFFRACTION100
2.8486-2.95040.30411360.21472594X-RAY DIFFRACTION100
2.9504-3.06850.25441350.20062565X-RAY DIFFRACTION100
3.0685-3.20810.22141390.18952630X-RAY DIFFRACTION100
3.2081-3.37720.22491360.18212582X-RAY DIFFRACTION100
3.3772-3.58870.23861360.18932588X-RAY DIFFRACTION100
3.5887-3.86570.21591370.17552611X-RAY DIFFRACTION100
3.8657-4.25450.22641380.17012618X-RAY DIFFRACTION100
4.2545-4.86950.20511390.16042641X-RAY DIFFRACTION100
4.8695-6.13290.24931390.19012643X-RAY DIFFRACTION100
6.1329-46.83480.2351440.20382739X-RAY DIFFRACTION99

+
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://pdbjlvh1.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