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- PDB-2bj1: NIKR IN OPEN CONFORMATION AND NICKEL BOUND TO HIGH-AFFINITY SITES -

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Basic information

Entry
Database: PDB / ID: 2bj1
TitleNIKR IN OPEN CONFORMATION AND NICKEL BOUND TO HIGH-AFFINITY SITES
ComponentsNICKEL RESPONSIVE REGULATOR
KeywordsTRANSCRIPTION / REPRESSOR / PYROCOCCUS HORIKOSHII / NIKR / DNA-BINDING / METAL-BINDING / NICKEL / TRANSCRIPTION REGULATION / 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
NICKEL (II) ION / Putative nickel-responsive regulator
Similarity search - Component
Biological speciesPYROCOCCUS HORIKOSHII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 27, 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9317
Polymers31,6612
Non-polymers2705
Water00
1
A: NICKEL RESPONSIVE REGULATOR
B: NICKEL RESPONSIVE REGULATOR
hetero molecules

A: NICKEL RESPONSIVE REGULATOR
B: NICKEL RESPONSIVE REGULATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,86214
Polymers63,3214
Non-polymers54010
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+3/21
MethodPQS
Unit cell
Length a, b, c (Å)99.893, 99.893, 97.978
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein NICKEL RESPONSIVE REGULATOR


Mass: 15830.320 Da / Num. of mol.: 2
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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
Compound detailsFUNCTION: POTENTIAL TRANSCRIPTIONAL REGULATOR

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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: 3.86 Å3/Da / Density % sol: 68.13 %
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 5, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 10315 / % possible obs: 99 % / Observed criterion σ(I): -1 / Redundancy: 9.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.8
Reflection shellResolution: 3→3.11 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 4.8 / % possible all: 98.8

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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 1Q5Y

1q5y


Resolution: 3→29.64 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1083324.61 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.281 877 4.7 %RANDOM
Rwork0.237 ---
obs0.237 18601 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.858 Å2 / ksol: 0.302503 e/Å3
Displacement parametersBiso mean: 81.1 Å2
Baniso -1Baniso -2Baniso -3
1-10.59 Å20 Å20 Å2
2--10.59 Å20 Å2
3----21.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.9 Å0.72 Å
Refinement stepCycle: LAST / Resolution: 3→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2132 0 5 0 2137
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.811.5
X-RAY DIFFRACTIONc_mcangle_it6.122
X-RAY DIFFRACTIONc_scbond_it5.722
X-RAY DIFFRACTIONc_scangle_it8.462.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.352 152 5 %
Rwork0.358 2870 -
obs--95.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP

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