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- PDB-2bj3: NIKR-apo -

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Basic information

Entry
Database: PDB / ID: 2bj3
TitleNIKR-apo
ComponentsNICKEL RESPONSIVE REGULATOR
KeywordsTRANSCRIPTION / REPRESSOR / PYROCOCCUS HORIKOSHII / NIKR / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI / STRUCTURAL GENOMICS
Function / homology
Function and homology information


response to nickel cation / nickel cation binding / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
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 ...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
Putative nickel-responsive regulator
Similarity search - Component
Biological speciesPYROCOCCUS HORIKOSHII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTahirov, T.H.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Structure of Pyrococcus Horikoshii Nikr: Nickel Sensing and Implications for the Regulation of DNA Recognition
Authors: Chivers, P.T. / Tahirov, T.H.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Crystallization and Preliminary Crystallographic Analysis of the Nickel-Responsive Regulator Nikr from Pyrococcus Horikoshii
Authors: Kitao, T. / Kuroishi, C. / Tahirov, T.H.
History
DepositionJan 28, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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

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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)63,4418
Polymers63,3214
Non-polymers1204
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)75.783, 54.322, 77.276
Angle α, β, γ (deg.)90.00, 116.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NICKEL RESPONSIVE REGULATOR


Mass: 15830.320 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS HORIKOSHII (archaea) / Strain: OT3 / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O58316
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growpH: 7.5 / Details: pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1
DetectorType: RIGAKU RAXIS-V / Detector: IMAGE PLATE / Date: Apr 10, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 28283 / % possible obs: 97.8 % / Observed criterion σ(I): -1 / Redundancy: 3.1 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.5 / % possible all: 94.7

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
DMphasing
CNSphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BJ1

2bj1


Resolution: 2.2→29.25 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1226247.43 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1415 5.1 %RANDOM
Rwork0.218 ---
obs0.218 28011 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.4958 Å2 / ksol: 0.338707 e/Å3
Displacement parametersBiso mean: 54.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.62 Å20 Å211.31 Å2
2--4.82 Å20 Å2
3----1.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4342 0 4 103 4449
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.63
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.961.5
X-RAY DIFFRACTIONc_mcangle_it5.72
X-RAY DIFFRACTIONc_scbond_it6.252
X-RAY DIFFRACTIONc_scangle_it8.682.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.453 222 5 %
Rwork0.392 4227 -
obs--93 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4MGO6.PARMGO6.TOP

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