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- PDB-1q5v: Apo-NikR -

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Basic information

Entry
Database: PDB / ID: 1q5v
TitleApo-NikR
ComponentsNickel responsive regulator
KeywordsTRANSCRIPTION / homotetramer / ribbon-helix-helix domain / beta sandwich
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 / Met repressor-like / Arc Repressor Mutant ...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 / 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
Nickel-responsive regulator
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Se-SAD / Resolution: 2.3 Å
AuthorsSchreiter, E.R. / Sintchak, M.D. / Guo, Y. / Chivers, P.T. / Sauer, R.T. / Drennan, C.L.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Crystal Structure of the Nickel-Responsive Transcription Factor NikR
Authors: Schreiter, E.R. / Sintchak, M.D. / Guo, Y. / Chivers, P.T. / Sauer, R.T. / Drennan, C.L.
History
DepositionAug 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)60,4754
Polymers60,4754
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11980 Å2
ΔGint-69 kcal/mol
Surface area23480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.360, 69.530, 158.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
DetailsThe biological assembly is a homotetramer. One biological homotetramer is present in the asymmetric unit.

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Components

#1: Protein
Nickel responsive regulator / NIKR


Mass: 15118.806 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: NIKR / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: P0A6Z6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.12 Å3/Da / Density % sol: 41.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 6000, magnesium chloride, N-(2-(acetamido)imino)diacetic acid (ADA), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18 mg/mlprotein1drop
220 mMTris1droppH8.0
3300 mM1dropNaCl
4100 mMADA1reservoirpH6.5
56 %(w/v)PEG60001reservoir
650 mM1reservoirMgCl2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 8-BM10.9791
SYNCHROTRONNSLS X2521.1
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJul 2, 2002
ADSC QUANTUM 3152CCDApr 11, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAGITALLY FOCUSED Si(220) DCMSINGLE WAVELENGTHMx-ray1
2Si(111) or (220)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
21.11
ReflectionResolution: 2.3→50 Å / Num. all: 23458 / Num. obs: 23458 / % possible obs: 99.2 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 10.7 % / Rsym value: 0.052 / Net I/σ(I): 27
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 5.8 / Rsym value: 0.359 / % possible all: 97.4
Reflection
*PLUS
Num. measured all: 250494 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 97.4 % / Rmerge(I) obs: 0.359

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: Se-SAD / Resolution: 2.3→38.57 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.305 1826 7.9 %RANDOM
Rwork0.248 ---
all0.253 23601 --
obs0.248 23161 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.3448 Å2 / ksol: 0.309638 e/Å3
Displacement parametersBiso mean: 65.6 Å2
Baniso -1Baniso -2Baniso -3
1--7.84 Å20 Å20 Å2
2---2.19 Å20 Å2
3---10.03 Å2
Refine analyzeLuzzati coordinate error free: 0.51 Å / Luzzati sigma a free: 0.49 Å
Refinement stepCycle: LAST / Resolution: 2.3→38.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3626 0 0 22 3648
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it3.521.5
X-RAY DIFFRACTIONc_mcangle_it5.352
X-RAY DIFFRACTIONc_scbond_it5.12
X-RAY DIFFRACTIONc_scangle_it7.082.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.469 264 7.2 %
Rwork0.39 3388 -
obs--94.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 50 Å / % reflection Rfree: 8 % / Rfactor Rwork: 0.247
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75

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