[English] 日本語
Yorodumi
- PDB-3bku: Apo C-terminal Domain of NikR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bku
TitleApo C-terminal Domain of NikR
ComponentsNickel-responsive regulator
KeywordsMETAL BINDING PROTEIN / NikR / nickel regulatory protein / transcription factor / beta sandwich / DNA-binding / Metal-binding / Repressor / Transcription regulation
Function / homology
Function and homology information


negative regulation of DNA-templated transcription initiation / response to nickel cation / DNA-binding transcription repressor activity / nickel cation binding / core promoter sequence-specific DNA binding / protein-DNA complex / transcription regulator complex / sequence-specific DNA binding / transcription cis-regulatory region binding / regulation of DNA-templated transcription ...negative regulation of DNA-templated transcription initiation / response to nickel cation / DNA-binding transcription repressor activity / nickel cation binding / core promoter sequence-specific DNA binding / protein-DNA complex / transcription regulator complex / sequence-specific DNA binding / transcription cis-regulatory region binding / regulation of DNA-templated transcription / DNA binding / identical protein binding
Similarity search - Function
Nickel-responsive transcriptional regulator NikR, proteobacteria / : / 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 / Arc-type ribbon-helix-helix ...Nickel-responsive transcriptional regulator NikR, proteobacteria / : / 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 / Arc-type ribbon-helix-helix / Ribbon-helix-helix / ACT-like domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nickel-responsive regulator
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsPhillips, C.M. / Schreiter, E.R. / Drennan, C.L.
CitationJournal: Biochemistry / Year: 2008
Title: Structural Basis of the Metal Specificity for Nickel Regulatory Protein NikR.
Authors: Phillips, C.M. / Schreiter, E.R. / Guo, Y. / Wang, S.C. / Zamble, D.B. / Drennan, C.L.
History
DepositionDec 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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: Nickel-responsive regulator
B: Nickel-responsive regulator
C: Nickel-responsive regulator
D: Nickel-responsive regulator


Theoretical massNumber of molelcules
Total (without water)38,8994
Polymers38,8994
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
MethodPISA
2
A: Nickel-responsive regulator
B: Nickel-responsive regulator


Theoretical massNumber of molelcules
Total (without water)19,4502
Polymers19,4502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
MethodPISA
3
C: Nickel-responsive regulator
D: Nickel-responsive regulator


Theoretical massNumber of molelcules
Total (without water)19,4502
Polymers19,4502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.350, 59.660, 75.140
Angle α, β, γ (deg.)90.000, 94.010, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Nickel-responsive regulator


Mass: 9724.845 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nikR, yhhG / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A6Z6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 1.94 Å3/Da / Density % sol: 36.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M Na Tartrate, 20% w/v PEG 3350, pH 8.0, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 6, 2004
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 17500 / Num. obs: 17408 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.08 / Rsym value: 0.069 / Χ2: 1.488 / Net I/σ(I): 17.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 1.7 / Num. unique all: 1686 / Rsym value: 0.451 / Χ2: 0.89 / % possible all: 96.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.004data extraction
MAR345dtbdata collection
EPMRphasing
RefinementStarting model: Ni-bound C-terminal domain of NikR (1Q5Y)

1q5y


Resolution: 2.1→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.336 1142 6.5 %RANDOM
Rwork0.288 ---
all0.291 17408 --
obs0.291 16783 95.9 %-
Solvent computationBsol: 65.922 Å2
Displacement parametersBiso mean: 62.113 Å2
Baniso -1Baniso -2Baniso -3
1-7.627 Å20 Å2-10.347 Å2
2--2.22 Å20 Å2
3----9.847 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2218 0 0 15 2233
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.7231.5
X-RAY DIFFRACTIONc_scbond_it1.9692
X-RAY DIFFRACTIONc_mcangle_it2.9962
X-RAY DIFFRACTIONc_scangle_it2.8772.5
LS refinement shellResolution: 2.1→2.18 Å / Num. reflection obs: 1685
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

+
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