[English] 日本語
Yorodumi
- PDB-7zge: BrxA, BREX phage defence protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zge
TitleBrxA, BREX phage defence protein
ComponentsBrxA, BREX phage defence protein
KeywordsANTIVIRAL PROTEIN / BREX Phage Defence Bacteriophage Exclusion
Function / homologyBrxA superfamily / BrxA / BrxA / Uncharacterized protein
Function and homology information
Biological speciesEscherichia fergusonii ATCC 35469 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsPicton, D.M. / Beck, I.N. / Blower, T.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other private United Kingdom
Citation
Journal: J.Struct.Biol. / Year: 2021
Title: Crystal structure of the anti-CRISPR repressor Aca2.
Authors: Usher, B. / Birkholz, N. / Beck, I.N. / Fagerlund, R.D. / Jackson, S.A. / Fineran, P.C. / Blower, T.R.
#1: Journal: Curr Res Struct Biol / Year: 2022
Title: Crystal structure of the BREX phage defence protein BrxA
Authors: Beck, I.N. / Picton, D.M. / Blower, T.R.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#3: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionApr 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Mar 20, 2024Group: Structure summary / Category: entity / struct / Item: _entity.pdbx_description / _struct.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BrxA, BREX phage defence protein
B: BrxA, BREX phage defence protein
C: BrxA, BREX phage defence protein


Theoretical massNumber of molelcules
Total (without water)68,3113
Polymers68,3113
Non-polymers00
Water3,639202
1
A: BrxA, BREX phage defence protein


Theoretical massNumber of molelcules
Total (without water)22,7701
Polymers22,7701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BrxA, BREX phage defence protein


Theoretical massNumber of molelcules
Total (without water)22,7701
Polymers22,7701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: BrxA, BREX phage defence protein


Theoretical massNumber of molelcules
Total (without water)22,7701
Polymers22,7701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)174.424, 42.539, 86.839
Angle α, β, γ (deg.)90.000, 102.744, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein BrxA, BREX phage defence protein / DUF1819 family protein


Mass: 22770.404 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia fergusonii ATCC 35469 (bacteria)
Strain: ATCC 35469 / DSM 13698 / CCUG 18766 / IAM 14443 / JCM 21226 / LMG 7866 / NBRC 102419 / NCTC 12128 / CDC 0568-73
Gene: EFER_p0021 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7L3Y4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2 M (NH4)2SO4, 0.1 M N-(2-acetamido)iminodiacetic acid (ADA, pH 6.5), 18% v/v PEG Smear High

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.09→42.53 Å / Num. obs: 37354 / % possible obs: 100 % / Redundancy: 1.9 % / Biso Wilson estimate: 39.51 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 4.4
Reflection shellResolution: 2.09→2.15 Å / Rmerge(I) obs: 0.374 / Num. unique obs: 2867 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
REFMAC1.18.2_3874refinement
PHENIX1.18.2_3874refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BHW

3bhw


Resolution: 2.09→42.53 Å / SU ML: 0.3379 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.8124
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2651 1801 4.83 %
Rwork0.2228 35479 -
obs0.2249 37280 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.78 Å2
Refinement stepCycle: LAST / Resolution: 2.09→42.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4663 0 0 202 4865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00844736
X-RAY DIFFRACTIONf_angle_d1.1166384
X-RAY DIFFRACTIONf_chiral_restr0.0539736
X-RAY DIFFRACTIONf_plane_restr0.0059793
X-RAY DIFFRACTIONf_dihedral_angle_d19.17021800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.150.37851250.35182637X-RAY DIFFRACTION97.25
2.15-2.210.35011230.33322738X-RAY DIFFRACTION100
2.21-2.280.35951420.31482663X-RAY DIFFRACTION100
2.28-2.360.33611460.27142754X-RAY DIFFRACTION100
2.36-2.460.31331350.26312689X-RAY DIFFRACTION100
2.46-2.570.28561400.25312712X-RAY DIFFRACTION99.96
2.57-2.70.29451440.2442709X-RAY DIFFRACTION100
2.7-2.870.29221380.24172719X-RAY DIFFRACTION100
2.87-3.10.28721390.23162729X-RAY DIFFRACTION100
3.1-3.410.28711270.22192744X-RAY DIFFRACTION99.97
3.41-3.90.23321500.19892764X-RAY DIFFRACTION100
3.9-4.910.20791490.17682754X-RAY DIFFRACTION100
4.91-42.530.24421430.20122867X-RAY DIFFRACTION99.93

+
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