[English] 日本語
Yorodumi
- PDB-2wvd: Structural and mechanistic insights into Helicobacter pylori NikR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wvd
TitleStructural and mechanistic insights into Helicobacter pylori NikR function
ComponentsPUTATIVE NICKEL-RESPONSIVE REGULATOR
KeywordsTRANSCRIPTION / TRANSCRIPTION FACTOR / TRANSCRIPTION REGULATION / RHH DNA-BINDING / METAL-BINDING / METALLOREGULATOR
Function / homology
Function and homology information


response to nickel cation / DNA-binding transcription repressor activity / nickel cation binding / protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / identical protein binding
Similarity search - Function
Transcription factor, NikR, nickel binding C-terminal / Nickel-responsive transcriptional regulator NikR / NikR C terminal nickel binding domain / ACT-like. Chain A, domain 2 / Acetolactate synthase/Transcription factor NikR, C-terminal / Ribbon-helix-helix protein, CopG / Ribbon-helix-helix protein, copG family / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix ...Transcription factor, NikR, nickel binding C-terminal / Nickel-responsive transcriptional regulator NikR / NikR C terminal nickel binding domain / ACT-like. Chain A, domain 2 / Acetolactate synthase/Transcription factor NikR, C-terminal / Ribbon-helix-helix protein, CopG / Ribbon-helix-helix protein, copG family / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Ribbon-helix-helix / ACT-like domain / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Putative nickel-responsive regulator
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsDian, C. / Bahlawane, C. / Muller, C. / Round, A. / Delay, C. / Fauquant, C. / Schauer, K. / de Reuse, H. / Michaud-Soret, I. / Terradot, L.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Structural and Mechanistic Insights Into Helicobacter Pylori Nikr Activation.
Authors: Bahlawane, C. / Dian, C. / Muller, C. / Round, A. / Fauquant, C. / Schauer, K. / De Reuse, H. / Terradot, L. / Michaud-Soret, I.
History
DepositionOct 16, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PUTATIVE NICKEL-RESPONSIVE REGULATOR
B: PUTATIVE NICKEL-RESPONSIVE REGULATOR
C: PUTATIVE NICKEL-RESPONSIVE REGULATOR
D: PUTATIVE NICKEL-RESPONSIVE REGULATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,74616
Polymers68,6174
Non-polymers1,12912
Water1,06359
1
C: PUTATIVE NICKEL-RESPONSIVE REGULATOR
D: PUTATIVE NICKEL-RESPONSIVE REGULATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9659
Polymers34,3082
Non-polymers6577
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-75.1 kcal/mol
Surface area13300 Å2
MethodPISA
2
A: PUTATIVE NICKEL-RESPONSIVE REGULATOR
B: PUTATIVE NICKEL-RESPONSIVE REGULATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7817
Polymers34,3082
Non-polymers4725
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-76.7 kcal/mol
Surface area13410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.970, 116.980, 123.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
PUTATIVE NICKEL-RESPONSIVE REGULATOR / HPNIKR


Mass: 17154.205 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Strain: 26695 / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O25896
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 96 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 96 TO SER ...ENGINEERED RESIDUE IN CHAIN A, CYS 96 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 96 TO SER ENGINEERED RESIDUE IN CHAIN C, CYS 96 TO SER ENGINEERED RESIDUE IN CHAIN D, CYS 96 TO SER

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.8 % / Description: NONE
Crystal growDetails: 0.4-0.7 M AMMONIUM SULFATE, 100 MM CITRATE PH 5-5.4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 28, 2009
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.65→46.32 Å / Num. obs: 21767 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Biso Wilson estimate: 48.78 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.1
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.6 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CA9

2ca9


Resolution: 2.65→38.958 Å / SU ML: 0.84 / σ(F): 1.18 / Phase error: 21.87 / Stereochemistry target values: ML
Details: THE STRUCTURE WAS REFINED USING FOBS+ AND FOBS- AND NOT FOBS TO VERIFY THE PRESENCE OF METAL IONS
RfactorNum. reflection% reflection
Rfree0.2308 2081 5.1 %
Rwork0.2051 --
obs0.2064 40515 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.295 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso mean: 52.49 Å2
Baniso -1Baniso -2Baniso -3
1--7.5169 Å20 Å20 Å2
2--1.5028 Å2-0 Å2
3---6.0142 Å2
Refinement stepCycle: LAST / Resolution: 2.65→38.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4261 0 66 59 4386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034368
X-RAY DIFFRACTIONf_angle_d0.7825881
X-RAY DIFFRACTIONf_dihedral_angle_d18.6591606
X-RAY DIFFRACTIONf_chiral_restr0.06683
X-RAY DIFFRACTIONf_plane_restr0.002751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6501-2.74480.3142180.28943848X-RAY DIFFRACTION100
2.7448-2.85470.27081830.26063860X-RAY DIFFRACTION100
2.8547-2.98450.28922240.25493861X-RAY DIFFRACTION100
2.9845-3.14180.27332380.23923828X-RAY DIFFRACTION100
3.1418-3.33860.25211950.22783905X-RAY DIFFRACTION100
3.3386-3.59620.21782300.1883821X-RAY DIFFRACTION100
3.5962-3.95780.21551690.17963883X-RAY DIFFRACTION100
3.9578-4.52970.18931960.15773875X-RAY DIFFRACTION99
4.5297-5.70410.18752120.17663776X-RAY DIFFRACTION99
5.7041-38.96230.2282160.21313777X-RAY DIFFRACTION98
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)
12.22740.48640.13153.117-0.62231.70880.054-0.28080.14470.20210.11430.1664-0.0433-0.108-00.1927-0.0107-0.01010.19750.01020.1311-29.037615.0133-48.6571
20.79350.8386-0.46732.2701-0.92471.798-0.0556-0.02680.0110.0446-0.0254-0.097-0.03890.044300.12480.0381-0.0360.16930.04560.2025-14.92596.9152-32.4653
31.6680.18120.09660.62350.2232.29040.0429-0.08170.0894-0.0466-0.09690.0087-0.10950.0245-00.19220.0072-0.00070.14110.02960.160416.1528-15.8488-15.5146
41.14460.1902-0.45381.3414-0.36761.18690.01070.0338-0.04840.01830.06140.0005-0.0486-0.095300.20390.0349-0.02680.26140.04810.23032.087-1.7498-26.1187
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A OR CHAIN B) AND RESSEQ 6:63
2X-RAY DIFFRACTION2(CHAIN A OR CHAIN B) AND RESSEQ 64:143
3X-RAY DIFFRACTION3(CHAIN C OR CHAIN D) AND RESSEQ 8:63
4X-RAY DIFFRACTION4(CHAIN C OR CHAIN D) AND RESSEQ 64:145

+
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