[English] 日本語
Yorodumi
- PDB-5fcl: Crystal structure of Cas1 from Pectobacterium atrosepticum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fcl
TitleCrystal structure of Cas1 from Pectobacterium atrosepticum
ComponentsCRISPR-associated endonuclease Cas1
KeywordsDNA BINDING PROTEIN / CRISPR / Cas / adaptation / integrase / structural plasticity / asymmetry / bacteriophages / plasmids / horizontal gene transfer
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / DNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / metal ion binding
Similarity search - Function
CRISPR-associated protein Cas1, YPEST subtype / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated protein Cas1 / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR associated protein Cas1 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L15; Chain: K; domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) ...CRISPR-associated protein Cas1, YPEST subtype / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated protein Cas1 / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR associated protein Cas1 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L15; Chain: K; domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CRISPR-associated endonuclease Cas1
Similarity search - Component
Biological speciesPectobacterium atrosepticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.7 Å
AuthorsWilkinson, M.E. / Nakatani, Y. / Opel-Reading, H.K. / Fineran, P.C. / Krause, K.L.
Funding support New Zealand, 5items
OrganizationGrant numberCountry
University of Otago New Zealand
Royal Society of New Zealand New Zealand
Otago School of Medical Sciences New Zealand
Health Research Council (HRC) New Zealand
Maurice Wilkins Centre New Zealand
CitationJournal: Biochem.J. / Year: 2016
Title: Structural plasticity and in vivo activity of Cas1 from the type I-F CRISPR-Cas system.
Authors: Wilkinson, M.E. / Nakatani, Y. / Staals, R.H. / Kieper, S.N. / Opel-Reading, H.K. / McKenzie, R.E. / Fineran, P.C. / Krause, K.L.
History
DepositionDec 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CRISPR-associated endonuclease Cas1
B: CRISPR-associated endonuclease Cas1
C: CRISPR-associated endonuclease Cas1
D: CRISPR-associated endonuclease Cas1
E: CRISPR-associated endonuclease Cas1
F: CRISPR-associated endonuclease Cas1


Theoretical massNumber of molelcules
Total (without water)226,2226
Polymers226,2226
Non-polymers00
Water3,765209
1
A: CRISPR-associated endonuclease Cas1
B: CRISPR-associated endonuclease Cas1


Theoretical massNumber of molelcules
Total (without water)75,4072
Polymers75,4072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-30 kcal/mol
Surface area25130 Å2
MethodPISA
2
C: CRISPR-associated endonuclease Cas1
D: CRISPR-associated endonuclease Cas1


Theoretical massNumber of molelcules
Total (without water)75,4072
Polymers75,4072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-28 kcal/mol
Surface area24580 Å2
MethodPISA
3
E: CRISPR-associated endonuclease Cas1
F: CRISPR-associated endonuclease Cas1


Theoretical massNumber of molelcules
Total (without water)75,4072
Polymers75,4072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-23 kcal/mol
Surface area24920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)261.359, 164.065, 78.685
Angle α, β, γ (deg.)90.00, 90.09, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
CRISPR-associated endonuclease Cas1


Mass: 37703.660 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672) (bacteria)
Strain: SCRI 1043 / ATCC BAA-672 / Gene: cas1, ECA3679 / Plasmid: pQE-80L derivative / Production host: Pectobacterium atrosepticum (bacteria) / Strain (production host): PCF80
References: UniProt: Q6D0X0, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 3.87 Å3/Da / Density % sol: 68.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.6 / Details: 100 mM Tris-HCl pH 8.6, 10% PEG6000, 0.1 mM SrCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.7→46.32 Å / Num. obs: 86942 / % possible obs: 95.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 49.27 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.127 / Net I/σ(I): 6
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 1.6 / Num. measured all: 15274 / Num. unique all: 4658 / CC1/2: 0.651 / Rpim(I) all: 0.4 / Rejects: 0 / % possible all: 97

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.10.1-2155refinement
REFMAC5.8.0049refinement
Aimless0.5.2data scaling
PHASER2.5.5phasing
PDB_EXTRACT3.15data extraction
XDS3 November 2014data scaling
RefinementResolution: 2.7→46.32 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.232 4233 4.9 %
Rwork0.188 --
obs-86931 95.8 %
Refinement stepCycle: LAST / Resolution: 2.7→46.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14133 0 0 209 14342
LS refinement shellResolution: 2.7→2.73 Å
RfactorNum. reflection
Rfree0.3352 -
Rwork0.2778 -
obs-82698

+
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