[English] 日本語
Yorodumi
- PDB-7ezy: anti-CRISPR-associated Aca2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ezy
Titleanti-CRISPR-associated Aca2
Componentsanti-CRISPR-associated Aca2
KeywordsIMMUNE SYSTEM / Aca2 / DNA BINDING PROTEIN / AUTOREGULATOR
Function / homologyPutative cytoplasmic protein / Putative cytoplasmic protein / Orthogonal Bundle / Mainly Alpha
Function and homology information
Biological speciesOceanimonas smirnovii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsLee, S.Y. / Park, H.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Molecular basis of transcriptional repression of anti-CRISPR by anti-CRISPR-associated 2.
Authors: Lee, S.Y. / Kim, G.E. / Park, H.H.
History
DepositionJun 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id ..._struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id
Revision 1.2Aug 6, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: anti-CRISPR-associated Aca2
B: anti-CRISPR-associated Aca2


Theoretical massNumber of molelcules
Total (without water)28,6602
Polymers28,6602
Non-polymers00
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-19 kcal/mol
Surface area12320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.130, 64.130, 135.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 68 or (resid 69...
d_2ens_1(chain "B" and (resid 1 through 29 or (resid 30...

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 1 - 124 / Label seq-ID: 1 - 124

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

-
Components

#1: Protein anti-CRISPR-associated Aca2


Mass: 14330.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oceanimonas smirnovii (bacteria) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 1000, 0.1M Tris base pH 8.9

-
Data collection

DiffractionMean temperature: 125 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→28.98 Å / Num. obs: 22344 / % possible obs: 99.8 % / Redundancy: 25.8 % / Biso Wilson estimate: 35.02 Å2 / Rrim(I) all: 0.1378 / Net I/σ(I): 19.56
Reflection shellResolution: 1.92→1.989 Å / Num. unique obs: 2162 / CC1/2: 0.669

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4a4a

4a4a


Resolution: 1.92→28.98 Å / SU ML: 0.2525 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.3996
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2319 1999 8.95 %
Rwork0.1976 20343 -
obs0.2007 22342 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.84 Å2
Refinement stepCycle: LAST / Resolution: 1.92→28.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1975 0 0 209 2184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00872009
X-RAY DIFFRACTIONf_angle_d1.17182730
X-RAY DIFFRACTIONf_chiral_restr0.0619311
X-RAY DIFFRACTIONf_plane_restr0.0094354
X-RAY DIFFRACTIONf_dihedral_angle_d5.4996275
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.573449747825 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.970.35031380.29441404X-RAY DIFFRACTION98.4
1.97-2.020.30981380.28461410X-RAY DIFFRACTION99.74
2.02-2.080.31251410.24221427X-RAY DIFFRACTION100
2.08-2.150.31741400.23031423X-RAY DIFFRACTION99.94
2.15-2.220.27011400.21731419X-RAY DIFFRACTION100
2.22-2.310.27691410.21521436X-RAY DIFFRACTION100
2.31-2.420.23921400.20511436X-RAY DIFFRACTION100
2.42-2.550.2841420.22081444X-RAY DIFFRACTION100
2.55-2.710.27931420.22321453X-RAY DIFFRACTION99.94
2.71-2.910.24751440.21121451X-RAY DIFFRACTION100
2.91-3.210.22341430.21311461X-RAY DIFFRACTION100
3.21-3.670.24021450.18151472X-RAY DIFFRACTION100
3.67-4.620.1841470.16051505X-RAY DIFFRACTION100
4.62-28.980.19551580.18551602X-RAY DIFFRACTION99.89

+
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