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- PDB-3bkf: Zinc-bound C-terminal Domain of NikR -

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Basic information

Entry
Database: PDB / ID: 3bkf
TitleZinc-bound 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 / 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: 1.9 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 6, 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 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nickel-responsive regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8563
Polymers9,7251
Non-polymers1312
Water39622
1
A: Nickel-responsive regulator
hetero molecules

A: Nickel-responsive regulator
hetero molecules

A: Nickel-responsive regulator
hetero molecules

A: Nickel-responsive regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,42312
Polymers38,8994
Non-polymers5238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z1
crystal symmetry operation4_455-x-1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area5640 Å2
MethodPISA
2
A: Nickel-responsive regulator
hetero molecules

A: Nickel-responsive regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7116
Polymers19,4502
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z1
Buried area1830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.220, 46.220, 124.900
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
DetailsBiological unit is a tetramer generated from the monomer in the asymmetric unit and is of the same tetrameric organization as in other C-terminal NikR structures.

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Components

#1: Protein Nickel-responsive regulator


Mass: 9724.845 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nikR / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A6Z6
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: 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: 1.98 Å3/Da / Density % sol: 37.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Bis-Tris, 0.2M Ammonium Sulfate, 25% w/v PEG 3350, pH 6.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.2829, 1.0
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 9, 2006
RadiationMonochromator: Si 111 Double-crystal monochrometer / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.28291
211
ReflectionResolution: 1.9→40 Å / Num. obs: 6755 / % possible obs: 99.5 % / Redundancy: 9.8 % / Rsym value: 0.52 / Net I/σ(I): 28.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 6 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 957 / Rsym value: 0.345

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Processing

Software
NameVersionClassificationNB
SCALAdata processing
CNSrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementStarting model: MONOMER OF PDB 1Q5Y

1q5y


Resolution: 1.9→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 564 4.8 %RANDOM
Rwork0.25 ---
all0.251 6789 --
obs0.251 6755 99.3 %-
Solvent computationBsol: 59.007 Å2
Displacement parametersBiso mean: 45.545 Å2
Baniso -1Baniso -2Baniso -3
1-2.155 Å2-2.315 Å20 Å2
2--2.155 Å20 Å2
3----4.311 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms508 0 2 22 532
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it2.2011.5
X-RAY DIFFRACTIONc_scbond_it2.2982
X-RAY DIFFRACTIONc_mcangle_it3.632
X-RAY DIFFRACTIONc_scangle_it3.7672.5
LS refinement shellResolution: 1.9→1.9 Å
RfactorNum. reflection% reflection
Rfree0.273 564 -
Rwork0.249 --
obs-11703 99.3 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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