[English] 日本語
Yorodumi
- PDB-5b7d: OxyR2 E204G mutant regulatory domain from Vibrio vulnificus (sulf... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5b7d
TitleOxyR2 E204G mutant regulatory domain from Vibrio vulnificus (sulfate-bound)
ComponentsLysR family transcriptional regulator
KeywordsTRANSCRIPTION / 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
Hydrogen peroxide-inducible genes activator
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 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
DepositionJun 7, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)48,4405
Polymers48,1522
Non-polymers2883
Water12,250680
1
A: LysR family transcriptional regulator
hetero molecules

A: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3444
Polymers48,1522
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3440 Å2
ΔGint-82 kcal/mol
Surface area19040 Å2
MethodPISA
2
B: LysR family transcriptional regulator
hetero molecules

B: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5366
Polymers48,1522
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3190 Å2
ΔGint-58 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.705, 137.238, 96.655
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: 24075.781 Da / Num. of mol.: 2 / Fragment: UNP residues 86-301 / Mutation: E204G
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 680 / 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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M ammonium sulfate, 0.1M sodium citrate (pH 5.6), 11% PEG 4000, 2mM TCEP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. obs: 74251 / % possible obs: 99.7 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 31.39
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.8 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B6U

5b6u
PDB Unreleased entry


Resolution: 1.52→19.756 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 15.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1831 3644 5 %
Rwork0.1573 --
obs0.1586 72860 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.52→19.756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3288 0 15 680 3983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083520
X-RAY DIFFRACTIONf_angle_d0.9644807
X-RAY DIFFRACTIONf_dihedral_angle_d4.033331
X-RAY DIFFRACTIONf_chiral_restr0.066570
X-RAY DIFFRACTIONf_plane_restr0.006633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5201-1.54010.22691100.20122026X-RAY DIFFRACTION76
1.5401-1.56120.2402950.20812377X-RAY DIFFRACTION87
1.5612-1.58350.2321390.20792520X-RAY DIFFRACTION93
1.5835-1.60710.23011310.20522564X-RAY DIFFRACTION96
1.6071-1.63220.23711330.20712660X-RAY DIFFRACTION98
1.6322-1.6590.2441550.19592651X-RAY DIFFRACTION99
1.659-1.68760.23981220.18972678X-RAY DIFFRACTION99
1.6876-1.71820.19611500.18252680X-RAY DIFFRACTION99
1.7182-1.75130.21911360.18232695X-RAY DIFFRACTION100
1.7513-1.7870.19521430.18532686X-RAY DIFFRACTION100
1.787-1.82580.20991480.17412702X-RAY DIFFRACTION100
1.8258-1.86830.20441390.16782679X-RAY DIFFRACTION100
1.8683-1.91490.18691450.15322696X-RAY DIFFRACTION100
1.9149-1.96670.17291450.15442708X-RAY DIFFRACTION100
1.9667-2.02450.16571390.15092697X-RAY DIFFRACTION100
2.0245-2.08980.19371590.15072691X-RAY DIFFRACTION100
2.0898-2.16440.17261470.14222700X-RAY DIFFRACTION100
2.1644-2.25090.16411560.14062705X-RAY DIFFRACTION100
2.2509-2.35320.16631270.14452751X-RAY DIFFRACTION100
2.3532-2.4770.16261360.1472723X-RAY DIFFRACTION100
2.477-2.63190.19661640.15222703X-RAY DIFFRACTION100
2.6319-2.83460.17521640.15742708X-RAY DIFFRACTION100
2.8346-3.11880.1761450.15242760X-RAY DIFFRACTION100
3.1188-3.56780.16751500.14662750X-RAY DIFFRACTION100
3.5678-4.48640.14881390.13222789X-RAY DIFFRACTION100
4.4864-19.75750.18781270.15472917X-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)
14.7851-2.00780.97150.8666-0.41280.20090.09750.45560.2191-0.0063-0.15-0.19290.01130.1730.03640.0891-0.01890.00160.17570.02420.146326.9473-6.340716.951
21.13910.2109-0.0260.4157-0.04270.8114-0.020.00010.0005-0.0470.0020.0021-0.04770.0480.01810.0957-0.00190.00140.0658-0.00490.06136.6268-5.987213.1672
31.4392-0.82530.10060.94230.01613.08330.03240.1486-0.1544-0.0831-0.02830.1741-0.1517-0.31590.04330.09310.0137-0.02440.1118-0.00040.1077-16.0707-4.971511.0065
40.82940.226-0.42520.5138-0.24020.6911-0.05390.0876-0.0678-0.08360.0075-0.04250.0279-0.01790.04730.0988-0.0036-0.00770.0828-0.00990.06640.658-10.635911.8419
53.5781-1.78920.10180.897-0.0521-0.00220.07460.3096-0.41980.0167-0.09870.21-0.0155-0.1681-0.02090.0989-0.02950.0120.2237-0.04710.1759-28.0709-41.509917.3913
61.1210.4647-0.11010.6907-0.04040.9281-0.05120.071-0.0259-0.06130.03070.02270.0943-0.10670.0220.0824-0.0144-0.00190.0856-0.01030.0745-8.3486-41.906914.1991
72.8461-0.635-0.96890.2482-0.25532.90150.07950.0946-0.018-0.0869-0.0536-0.05130.14430.24910.03110.12280.03130.03460.1022-0.01360.106714.5207-42.829.3607
81.19910.34880.24350.67740.08110.7141-0.03850.14970.0562-0.07380.00820.07170.0646-0.02920.03090.0694-0.00610.00830.07860.00160.0573-2.1421-37.142111.8548
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 180 )
3X-RAY DIFFRACTION3chain 'A' and (resid 181 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 180 )
7X-RAY DIFFRACTION7chain 'B' and (resid 181 through 230 )
8X-RAY DIFFRACTION8chain '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://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