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- PDB-3bku: Apo C-terminal Domain of NikR -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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)
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

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