[English] 日本語
Yorodumi
- PDB-3pqj: Crystal Structure of the transcriptional repressor BigR from Xyle... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pqj
TitleCrystal Structure of the transcriptional repressor BigR from Xylella fastidiosa
ComponentsBiofilm growth-associated repressor
KeywordsTRANSCRIPTION / helix-turn-helix motif / winged-helix fold / transcriptional repressor / DNA binding
Function / homology
Function and homology information


DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription
Similarity search - Function
Helix-turn-helix domain / ArsR-type HTH domain profile. / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biofilm growth-associated repressor
Similarity search - Component
Biological speciesXylella fastidiosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsGuimaraes, B.G. / Benedetti, C.E.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Plant Pathogenic Bacteria Utilize Biofilm Growth-associated Repressor (BigR), a Novel Winged-helix Redox Switch, to Control Hydrogen Sulfide Detoxification under Hypoxia.
Authors: Guimaraes, B.G. / Barbosa, R.L. / Soprano, A.S. / Campos, B.M. / de Souza, T.A. / Tonoli, C.C. / Leme, A.F. / Murakami, M.T. / Benedetti, C.E.
History
DepositionNov 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Database references
Revision 1.3Feb 21, 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: Biofilm growth-associated repressor
B: Biofilm growth-associated repressor
C: Biofilm growth-associated repressor
D: Biofilm growth-associated repressor


Theoretical massNumber of molelcules
Total (without water)46,0774
Polymers46,0774
Non-polymers00
Water2,324129
1
A: Biofilm growth-associated repressor
B: Biofilm growth-associated repressor


Theoretical massNumber of molelcules
Total (without water)23,0392
Polymers23,0392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-30 kcal/mol
Surface area9800 Å2
MethodPISA
2
C: Biofilm growth-associated repressor
D: Biofilm growth-associated repressor


Theoretical massNumber of molelcules
Total (without water)23,0392
Polymers23,0392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-31 kcal/mol
Surface area9850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.590, 47.840, 54.700
Angle α, β, γ (deg.)90.03, 89.96, 105.34
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Biofilm growth-associated repressor


Mass: 11519.313 Da / Num. of mol.: 4 / Fragment: UNP residues 13-114
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xylella fastidiosa (bacteria) / Gene: bigR, XF_0767 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9PFB1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.22 Å3/Da / Density % sol: 44.67 %

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4333 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 12, 2008
RadiationMonochromator: Si 111 DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4333 Å / Relative weight: 1
ReflectionResolution: 2.48→45 Å / Num. all: 14053 / Num. obs: 13185 / % possible obs: 93.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.88 % / Biso Wilson estimate: 51.27 Å2 / Net I/σ(I): 13.22
Reflection shellResolution: 2.48→2.63 Å / Mean I/σ(I) obs: 3.97 / Num. unique all: 1885 / % possible all: 83.8

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
BUSTER2.9.1refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→20.86 Å / SU R Cruickshank DPI: 0.873 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2499 659 5 %RANDOM
Rwork0.194 ---
all0.1967 ---
obs0.1967 13169 93.9 %-
Displacement parametersBiso mean: 43.35 Å2
Refine analyzeLuzzati coordinate error obs: 0.318 Å
Refinement stepCycle: LAST / Resolution: 2.48→20.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2923 0 0 129 3052
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0129472
X-RAY DIFFRACTIONt_angle_deg1.1739752
X-RAY DIFFRACTIONt_dihedral_angle_d10792
X-RAY DIFFRACTIONt_trig_c_planes802
X-RAY DIFFRACTIONt_gen_planes4235
X-RAY DIFFRACTIONt_it294720
X-RAY DIFFRACTIONt_omega_torsion2.75
X-RAY DIFFRACTIONt_other_torsion18
X-RAY DIFFRACTIONt_chiral_improper_torsion4055
X-RAY DIFFRACTIONt_ideal_dist_contact34834
LS refinement shellResolution: 2.48→2.68 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.3135 125 5.01 %
Rwork0.2155 2368 -
all0.2202 2493 -
obs--93.9 %

+
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