[English] 日本語
Yorodumi
- PDB-5x0v: Reduced form of regulatory domain of OxyR2 from Vibrio vulnificus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5x0v
TitleReduced form of regulatory domain of OxyR2 from Vibrio vulnificus
ComponentsLysR family transcriptional regulator
KeywordsDNA BINDING PROTEIN / LysR-type transcription regulator / LTTR / OxyR / H2O2
Function / homology
Function and homology information


protein-DNA complex / DNA-binding transcription factor activity
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Hydrogen peroxide-inducible genes activator
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsJo, I. / Ha, N.-C.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: The hydrogen peroxide hypersensitivity of OxyR2 in Vibrio vulnificus depends on conformational constraints
Authors: Jo, I. / Kim, D. / Bang, Y.-J. / Ahn, J. / Choi, S.H. / Ha, N.-C.
History
DepositionJan 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Mar 20, 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: LysR family transcriptional regulator
B: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5595
Polymers48,2962
Non-polymers2633
Water7,927440
1
A: LysR family transcriptional regulator
hetero molecules

A: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3674
Polymers48,2962
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3030 Å2
ΔGint-41 kcal/mol
Surface area18940 Å2
MethodPISA
2
B: LysR family transcriptional regulator
hetero molecules

B: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7516
Polymers48,2962
Non-polymers4554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3440 Å2
ΔGint-42 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.204, 138.348, 97.473
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein LysR family transcriptional regulator / OxyR2


Mass: 24147.844 Da / Num. of mol.: 2 / Fragment: UNP residues 86-301
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: MO6-24/O / Production host: Escherichia coli (E. coli) / References: UniProt: A0A087I947
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M ammonium citrate (pH 6.5), 14% (w/v) PEG 3350, 2mM TCEP (Tris(2-carboxyethyl)phosphine), 5mM DTT

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 62093 / % possible obs: 98.7 % / Redundancy: 8 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.027 / Net I/σ(I): 18.6
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.45 / Num. unique all: 2958 / Rpim(I) all: 0.164 / % possible all: 95.5

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
DENZOdata reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→48.736 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 17.74
RfactorNum. reflection% reflection
Rfree0.1916 2869 5.16 %
Rwork0.1593 --
obs0.161 55578 88.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→48.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 15 440 3761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153459
X-RAY DIFFRACTIONf_angle_d1.314717
X-RAY DIFFRACTIONf_dihedral_angle_d5.7922941
X-RAY DIFFRACTIONf_chiral_restr0.095562
X-RAY DIFFRACTIONf_plane_restr0.008620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5992-1.62680.2523630.20231130X-RAY DIFFRACTION39
1.6268-1.65640.2118730.21361451X-RAY DIFFRACTION49
1.6564-1.68820.2656950.20261696X-RAY DIFFRACTION58
1.6882-1.72270.2381170.20162019X-RAY DIFFRACTION69
1.7227-1.76010.22451170.19952376X-RAY DIFFRACTION79
1.7601-1.80110.23861390.1972618X-RAY DIFFRACTION88
1.8011-1.84610.21581340.19782802X-RAY DIFFRACTION95
1.8461-1.8960.23661550.1822853X-RAY DIFFRACTION97
1.896-1.95180.2151410.17962908X-RAY DIFFRACTION98
1.9518-2.01480.20591830.16082894X-RAY DIFFRACTION99
2.0148-2.08680.19791670.15532933X-RAY DIFFRACTION99
2.0868-2.17040.191630.14692952X-RAY DIFFRACTION99
2.1704-2.26920.1821590.14522965X-RAY DIFFRACTION99
2.2692-2.38880.19191550.14942953X-RAY DIFFRACTION99
2.3888-2.53850.20371710.1512946X-RAY DIFFRACTION99
2.5385-2.73450.22421460.15833020X-RAY DIFFRACTION100
2.7345-3.00960.1721630.15923003X-RAY DIFFRACTION100
3.0096-3.4450.18281530.15463022X-RAY DIFFRACTION100
3.445-4.33990.14462020.1383018X-RAY DIFFRACTION100
4.3399-48.75910.1861730.14693150X-RAY DIFFRACTION100
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)
13.3814-1.62311.06520.7747-0.51210.33840.09540.538-0.0559-0.0691-0.1572-0.2850.06180.2847-0.00160.07160.0009-0.01460.1830.00250.186526.2746-6.44816.6062
21.03130.271-0.22520.9226-0.04051.0331-0.05250.0306-0.0436-0.11140.0191-0.03290.0039-0.0230.01850.0614-0.0083-0.00860.0491-0.00890.04846.1774-6.191513.2839
30.6354-0.58180.02810.6176-0.3831.53610.07740.3064-0.1172-0.1717-0.01630.2722-0.0505-0.40220.08750.1170.009-0.06380.23090.00360.1529-16.1168-4.922411.7358
40.45980.1557-0.13320.8022-0.01160.6963-0.11190.1894-0.0926-0.14010.032-0.02420.0763-0.08690.02820.0825-0.0171-0.01640.0821-0.01270.05790.1172-10.883112.0662
56.4101-2.2864-0.75470.81320.26830.0880.09920.6318-0.11260.0566-0.16190.29530.0301-0.22650.02130.1024-0.02250.01680.1733-0.03370.2391-27.3974-41.61417.6302
61.6125-0.1744-0.26031.74790.66771.39180.01350.03950.1668-0.1513-0.0360.1791-0.0757-0.09190.01890.0781-0.0183-0.01140.0552-0.01080.0891-12.7981-40.847918.2603
72.7751.52410.20771.91510.10190.6127-0.03670.2071-0.0551-0.21340.0251-0.02450.04580.05750.00730.12550.00290.00830.08250.00510.0612-2.2776-42.298810.5144
80.94840.1854-0.23420.0518-0.17921.57220.03970.3372-0.0207-0.3153-0.0283-0.24710.18460.24320.12420.19640.02480.11130.2047-0.00760.168414.2643-43.10529.648
90.61850.37630.23061.0046-0.11670.3411-0.0830.22830.1879-0.1730.02620.09050.01850.04680.02340.1184-0.00270.01360.10030.02340.0871-1.8384-37.104712.23
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 83 through 105 )
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 181 )
3X-RAY DIFFRACTION3chain 'A' and (resid 182 through 230 )
4X-RAY DIFFRACTION4chain 'A' and (resid 231 through 301 )
5X-RAY DIFFRACTION5chain 'B' and (resid 83 through 105 )
6X-RAY DIFFRACTION6chain 'B' and (resid 106 through 144 )
7X-RAY DIFFRACTION7chain 'B' and (resid 145 through 180 )
8X-RAY DIFFRACTION8chain 'B' and (resid 181 through 230 )
9X-RAY DIFFRACTION9chain 'B' and (resid 231 through 301 )

+
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