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- PDB-1q5y: Nickel-Bound C-terminal Regulatory Domain of NikR -

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Basic information

Entry
Database: PDB / ID: 1q5y
TitleNickel-Bound C-terminal Regulatory Domain of NikR
ComponentsNickel responsive regulator
KeywordsMETAL BINDING PROTEIN / Nickel binding / regulatory 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 / 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 (II) ION / Nickel-responsive regulator
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,89213
Polymers38,3474
Non-polymers5459
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8480 Å2
ΔGint-87 kcal/mol
Surface area13440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.849, 78.287, 81.386
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
DetailsThe biological assembly of this protein is a homotetramer. There is one biological homotetramer in the asymmetric unit.

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Components

#1: Protein
Nickel responsive regulator / NikR


Mass: 9586.698 Da / Num. of mol.: 4 / Fragment: C-terminal domain of NikR
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: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 1.77 Å3/Da / Density % sol: 35.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 3350, di-sodium tartrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
220 mMTris1droppH8.0
3300 mM1dropNaCl
40.2 Mdisodium tartrate1reservoir
520 %(w/v)PEG33501reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.211.4852, 0.9500
SYNCHROTRONNSLS X2521.1
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDAug 1, 2002
ADSC QUANTUM 3152CCDJul 2, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double-crystal, Si(111)MADMx-ray1
2Si(111) or (220)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.48521
20.951
31.11
ReflectionResolution: 1.4→50 Å / Num. all: 57926 / Num. obs: 57926 / % possible obs: 99.2 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 6.2 % / Rsym value: 0.062 / Net I/σ(I): 17.5
Reflection shellResolution: 1.4→1.45 Å / Mean I/σ(I) obs: 3.7 / Rsym value: 0.31 / % possible all: 94.2
Reflection
*PLUS
Highest resolution: 1.4 Å / Num. measured all: 360689 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 94.2 % / Rmerge(I) obs: 0.31

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.4→10 Å / Num. parameters: 25203 / Num. restraintsaints: 31118 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.065
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 2865 5.2 %RANDOM
Rwork0.1602 ---
all0.1626 54886 --
obs0.1602 54886 94.3 %-
Refine analyzeNum. disordered residues: 9 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2776
Refinement stepCycle: LAST / Resolution: 1.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2522 0 24 253 2799
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0286
X-RAY DIFFRACTIONs_zero_chiral_vol0.054
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.066
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.022
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.04
X-RAY DIFFRACTIONs_approx_iso_adps0.089
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 10 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.22 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS

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