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- PDB-2hzv: NikR-operator DNA complex -

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Basic information

Entry
Database: PDB / ID: 2hzv
TitleNikR-operator DNA complex
Components
  • 5'-D(*AP*GP*TP*AP*TP*GP*AP*CP*GP*AP*AP*TP*AP*CP*TP*TP*AP*AP*AP*AP*TP*CP*GP*TP*CP*AP*TP*AP*CP*T)-3'
  • 5'-D(*AP*GP*TP*AP*TP*GP*AP*CP*GP*AP*TP*TP*TP*TP*AP*AP*GP*TP*AP*TP*TP*CP*GP*TP*CP*AP*TP*AP*CP*T)-3'
  • Nickel-responsive regulator
KeywordsMETAL BINDING PROTEIN/DNA / nickel / transcription factor / protein-dna complex / ribbon-helix-helix / METAL BINDING PROTEIN-DNA COMPLEX
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 (II) ION / DNA / DNA (> 10) / Nickel-responsive regulator
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Molecular Replacement/SAD / Resolution: 3.1 Å
AuthorsSchreiter, E.R. / Drennan, C.L.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: NikR-operator complex structure and the mechanism of repressor activation by metal ions.
Authors: Schreiter, E.R. / Wang, S.C. / Zamble, D.B. / Drennan, C.L.
History
DepositionAug 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / 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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: 5'-D(*AP*GP*TP*AP*TP*GP*AP*CP*GP*AP*AP*TP*AP*CP*TP*TP*AP*AP*AP*AP*TP*CP*GP*TP*CP*AP*TP*AP*CP*T)-3'
J: 5'-D(*AP*GP*TP*AP*TP*GP*AP*CP*GP*AP*TP*TP*TP*TP*AP*AP*GP*TP*AP*TP*TP*CP*GP*TP*CP*AP*TP*AP*CP*T)-3'
K: 5'-D(*AP*GP*TP*AP*TP*GP*AP*CP*GP*AP*AP*TP*AP*CP*TP*TP*AP*AP*AP*AP*TP*CP*GP*TP*CP*AP*TP*AP*CP*T)-3'
L: 5'-D(*AP*GP*TP*AP*TP*GP*AP*CP*GP*AP*TP*TP*TP*TP*AP*AP*GP*TP*AP*TP*TP*CP*GP*TP*CP*AP*TP*AP*CP*T)-3'
A: Nickel-responsive regulator
B: Nickel-responsive regulator
C: Nickel-responsive regulator
D: Nickel-responsive regulator
E: Nickel-responsive regulator
F: Nickel-responsive regulator
G: Nickel-responsive regulator
H: Nickel-responsive regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,48231
Polymers158,58312
Non-polymers90019
Water00
1
I: 5'-D(*AP*GP*TP*AP*TP*GP*AP*CP*GP*AP*AP*TP*AP*CP*TP*TP*AP*AP*AP*AP*TP*CP*GP*TP*CP*AP*TP*AP*CP*T)-3'
J: 5'-D(*AP*GP*TP*AP*TP*GP*AP*CP*GP*AP*TP*TP*TP*TP*AP*AP*GP*TP*AP*TP*TP*CP*GP*TP*CP*AP*TP*AP*CP*T)-3'
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)79,72215
Polymers79,2916
Non-polymers4309
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
K: 5'-D(*AP*GP*TP*AP*TP*GP*AP*CP*GP*AP*AP*TP*AP*CP*TP*TP*AP*AP*AP*AP*TP*CP*GP*TP*CP*AP*TP*AP*CP*T)-3'
L: 5'-D(*AP*GP*TP*AP*TP*GP*AP*CP*GP*AP*TP*TP*TP*TP*AP*AP*GP*TP*AP*TP*TP*CP*GP*TP*CP*AP*TP*AP*CP*T)-3'
E: Nickel-responsive regulator
F: Nickel-responsive regulator
G: Nickel-responsive regulator
H: Nickel-responsive regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,76116
Polymers79,2916
Non-polymers46910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)197.203, 76.132, 132.092
Angle α, β, γ (deg.)90.00, 110.27, 90.00
Int Tables number5
Space group name H-MC121
DetailsThere are two biological assemblies per asu. One biological assembly is a tetramer of NikR and a double-stranded DNA 30-mer.

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Components

#1: DNA chain 5'-D(*AP*GP*TP*AP*TP*GP*AP*CP*GP*AP*AP*TP*AP*CP*TP*TP*AP*AP*AP*AP*TP*CP*GP*TP*CP*AP*TP*AP*CP*T)-3'


Mass: 9213.992 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain 5'-D(*AP*GP*TP*AP*TP*GP*AP*CP*GP*AP*TP*TP*TP*TP*AP*AP*GP*TP*AP*TP*TP*CP*GP*TP*CP*AP*TP*AP*CP*T)-3'


Mass: 9226.974 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein
Nickel-responsive regulator


Mass: 15212.597 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nikR / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6Z6
#4: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ni
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: K

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 200 mM KCl, 50 mM MgCl2, 50 mM Tris pH 7.5, and 10% w/v PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1KCl11
2MgCl211
3Tris11
4PEG 400011
5PEG 400012
6MgCl212
7KCl12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0000, 0.9793
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 8, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97931
ReflectionResolution: 3.1→49.3 Å / Num. all: 32128 / Num. obs: 30232 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.1→3.21 Å / % possible all: 70.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
SOLVEphasing
RefinementMethod to determine structure: Molecular Replacement/SAD
Starting model: 1Q5Y, 1Q5V

1q5y

1q5v


Resolution: 3.1→49.28 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 203563.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.303 2119 7 %RANDOM
Rwork0.261 ---
all0.261 32128 --
obs0.261 30232 94.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.3218 Å2 / ksol: 0.245512 e/Å3
Displacement parametersBiso mean: 99.4 Å2
Baniso -1Baniso -2Baniso -3
1-43.12 Å20 Å2-4.96 Å2
2--1.75 Å20 Å2
3----44.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.84 Å0.72 Å
Refinement stepCycle: LAST / Resolution: 3.1→49.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8034 2448 19 0 10501
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_mcbond_it5.161.5
X-RAY DIFFRACTIONc_mcangle_it8.632
X-RAY DIFFRACTIONc_scbond_it7.552
X-RAY DIFFRACTIONc_scangle_it11.182.5
LS refinement shellHighest resolution: 3.1 Å / Total num. of bins used: 6 /
Num. reflection% reflection
Rwork3380 -
Rfree-6.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3ion.paramion.top

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