[English] 日本語
Yorodumi
- PDB-7xi5: Anti-CRISPR-associated Aca10 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xi5
TitleAnti-CRISPR-associated Aca10
ComponentsTranscriptional regulator
KeywordsIMMUNE SYSTEM / Aca10 / DNA BINDING PROTEIN / AUTOREGULATOR
Function / homologyCro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / DNA binding / Transcriptional regulator
Function and homology information
Biological speciesPseudomonas citronellolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsLee, S.Y. / Park, H.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Molecular basis of anti-CRISPR operon repression by Aca10.
Authors: Lee, S.Y. / Birkholz, N. / Fineran, P.C. / Park, H.H.
History
DepositionApr 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcriptional regulator
B: Transcriptional regulator
C: Transcriptional regulator
D: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)28,4324
Polymers28,4324
Non-polymers00
Water3,999222
1
A: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)7,1081
Polymers7,1081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)7,1081
Polymers7,1081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)7,1081
Polymers7,1081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)7,1081
Polymers7,1081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.920, 109.920, 60.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 44 or (resid 45...
d_2ens_1(chain "B" and (resid 3 through 33 or (resid 34...
d_3ens_1(chain "C" and (resid 3 through 33 or (resid 34...
d_4ens_1(chain "D" and (resid 3 through 44 or (resid 45...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERGLNA1 - 57
d_21ens_1SERGLNB1 - 57
d_31ens_1SERGLNC1 - 57
d_41ens_1SERGLND1 - 57

NCS oper:
IDCodeMatrixVector
1given(-0.999352439448, 0.0241038031916, -0.0267153222016), (0.0283698699056, 0.0711354888507, -0.997063133762), (-0.0221326060412, -0.997175385225, -0.0717732460751)41.8936841059, 73.0958131158, 79.4861207205
2given(-0.0662848012867, 0.997604770268, 0.0197749198859), (0.0825691150815, 0.0252345965419, -0.996265806084), (-0.994378532729, -0.0644044833493, -0.0840440132994)-12.2603408387, 60.8038334662, 26.6991452827
3given(-0.0972320129112, -0.994187442777, -0.0462305557922), (-0.0385529305526, 0.0501781477312, -0.997995904318), (0.994514759675, -0.0952548272471, -0.0432077617457)99.403648322, 89.0606595373, 30.4535914326

-
Components

#1: Protein
Transcriptional regulator / anti-CRISPR-associated Aca10


Mass: 7108.080 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas citronellolis (bacteria) / Gene: CW310_07415 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4Z0IPS5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 3.23 Å3/Da / Density % sol: 61.88 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 12% (v/v) 2-propanol, 0.1M Imidazole pH7.8

-
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: Aug 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→29.27 Å / Num. obs: 37421 / % possible obs: 99.94 % / Redundancy: 26.4 % / Biso Wilson estimate: 36.24 Å2 / CC1/2: 1 / Net I/σ(I): 25.08
Reflection shellResolution: 1.76→1.823 Å / Num. unique obs: 3674 / CC1/2: 0.56

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5j9i

5j9i


Resolution: 1.76→29.27 Å / SU ML: 0.2438 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.8135
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2262 1872 5 %
Rwork0.2078 35548 -
obs0.2088 37420 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.48 Å2
Refinement stepCycle: LAST / Resolution: 1.76→29.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 0 222 1984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00751806
X-RAY DIFFRACTIONf_angle_d0.95752463
X-RAY DIFFRACTIONf_chiral_restr0.0505280
X-RAY DIFFRACTIONf_plane_restr0.0095309
X-RAY DIFFRACTIONf_dihedral_angle_d3.5836237
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.303391983126
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.400138868011
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.506586795751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.810.35711410.34972679X-RAY DIFFRACTION99.89
1.81-1.860.37341420.32362693X-RAY DIFFRACTION100
1.86-1.920.32881420.28342689X-RAY DIFFRACTION100
1.92-1.990.28661410.26942690X-RAY DIFFRACTION100
1.99-2.070.2761430.25762709X-RAY DIFFRACTION99.96
2.07-2.160.2831430.24782709X-RAY DIFFRACTION100
2.16-2.280.31511420.23482698X-RAY DIFFRACTION100
2.28-2.420.25391430.22952719X-RAY DIFFRACTION100
2.42-2.610.27631430.24022725X-RAY DIFFRACTION100
2.61-2.870.21721440.21882740X-RAY DIFFRACTION100
2.87-3.280.23491460.21742763X-RAY DIFFRACTION99.97
3.28-4.130.19791460.1822790X-RAY DIFFRACTION100
4.14-29.270.17731560.16962944X-RAY DIFFRACTION99.94

+
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://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