[English] 日本語
Yorodumi
- PDB-6as4: Structure of a phage anti-CRISPR protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6as4
TitleStructure of a phage anti-CRISPR protein
ComponentsNHis AcrE1 anti-crispr protein
KeywordsVIRAL PROTEIN / phage protein
Function / homologyUncharacterized protein
Function and homology information
Biological speciesPseudomonas phage JBD5 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShah, M. / Calmettes, C. / Pawluk, A. / Mejdani, M. / Davidson, A.R. / Maxwell, K.L. / Moraes, T.F.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-130482 Canada
Canadian Institutes of Health Research (CIHR)MOP-136845 Canada
CitationJournal: MBio / Year: 2017
Title: Disabling a Type I-E CRISPR-Cas Nuclease with a Bacteriophage-Encoded Anti-CRISPR Protein.
Authors: Pawluk, A. / Shah, M. / Mejdani, M. / Calmettes, C. / Moraes, T.F. / Davidson, A.R. / Maxwell, K.L.
History
DepositionAug 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NHis AcrE1 anti-crispr protein
B: NHis AcrE1 anti-crispr protein
C: NHis AcrE1 anti-crispr protein


Theoretical massNumber of molelcules
Total (without water)36,3653
Polymers36,3653
Non-polymers00
Water2,702150
1
A: NHis AcrE1 anti-crispr protein
B: NHis AcrE1 anti-crispr protein


Theoretical massNumber of molelcules
Total (without water)24,2432
Polymers24,2432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-40 kcal/mol
Surface area10850 Å2
MethodPISA
2
C: NHis AcrE1 anti-crispr protein

C: NHis AcrE1 anti-crispr protein


Theoretical massNumber of molelcules
Total (without water)24,2432
Polymers24,2432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3650 Å2
ΔGint-42 kcal/mol
Surface area10760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.740, 63.530, 59.460
Angle α, β, γ (deg.)90.000, 100.340, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein NHis AcrE1 anti-crispr protein / phage anti-CRISPR protein


Mass: 12121.561 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Phage / Source: (gene. exp.) Pseudomonas phage JBD5 (virus) / Gene: JBD5_034 / Plasmid: pET21d(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: L7P7L6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2M ammonium citrate dibasic, 20% PEG3350

-
Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→47.585 Å / Num. obs: 23742 / % possible obs: 98.5 % / Redundancy: 7.7 % / Biso Wilson estimate: 37.05 Å2 / Rmerge(I) obs: 0.1033 / Net I/σ(I): 11.2
Reflection shellResolution: 2→2.071 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.596 / Mean I/σ(I) obs: 1.57 / CC1/2: 0.529 / % possible all: 97.59

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.22data extraction
XDSdata processing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AcrE1_CHis

Resolution: 2→47.585 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.65
RfactorNum. reflection% reflection
Rfree0.2284 1188 5.01 %
Rwork0.1895 --
obs0.1915 23721 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 144.89 Å2 / Biso mean: 48.1355 Å2 / Biso min: 22.15 Å2
Refinement stepCycle: final / Resolution: 2→47.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 0 150 2348
Biso mean---45.34 -
Num. residues----278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082300
X-RAY DIFFRACTIONf_angle_d0.9283117
X-RAY DIFFRACTIONf_chiral_restr0.038346
X-RAY DIFFRACTIONf_plane_restr0.004415
X-RAY DIFFRACTIONf_dihedral_angle_d14.901868
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.0910.34371450.30682741288697
2.091-2.20130.26861470.25462799294698
2.2013-2.33920.25181480.23772795294398
2.3392-2.51980.25631470.2152793294098
2.5198-2.77330.26821490.20642834298399
2.7733-3.17460.23891480.19852822297099
3.1746-3.99930.22511500.16962849299999
3.9993-47.59840.18351540.15742900305499
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.57861.12290.3282.69261.23071.5765-0.12720.26340.05170.02370.10460.22440.0247-0.01360.01190.22210.01330.00190.27190.06260.2541-29.68480.008822.4415
21.51650.6091-0.44962.69041.0752.2179-0.21160.43360.0333-0.36180.4099-0.0967-0.33850.2317-0.18240.2759-0.05740.02270.36880.04410.2711-18.59464.520218.9392
33.5673-0.0261.31363.14530.03792.41390.2212-0.0372-0.36770.17850.0274-0.07820.16280.1312-0.09270.2528-0.0054-0.01380.23420.00310.26745.17271.91823.6064
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 3:96)A3 - 96
2X-RAY DIFFRACTION2(chain B and resid 3:92)B3 - 92
3X-RAY DIFFRACTION3(chain C and resid 2:94)C2 - 94

+
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