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- PDB-2wvf: Structural and mechanistic insights into Helicobacter pylori NikR... -

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Basic information

Entry
Database: PDB / ID: 2wvf
TitleStructural and mechanistic insights into Helicobacter pylori NikR function
ComponentsPUTATIVE NICKEL-RESPONSIVE REGULATOR
KeywordsTRANSCRIPTION / TRANSCRIPTION FACTOR / TRANSCRIPTION REGULATION / RHH / NIKR / DNA-BINDING / METAL-BINDING / METALLOREGULATOR
Function / homology
Function and homology information


response to nickel cation / DNA-binding transcription repressor activity / nickel cation binding / protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / identical protein 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
FORMIC ACID / NICKEL (II) ION / Putative nickel-responsive regulator
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDian, C. / Bahlawane, C. / Muller, C. / Round, A. / Delay, C. / Fauquant, C. / Schauer, K. / de Reuse, H. / Michaud-Soret, I. / Terradot, L.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Structural and Mechanistic Insights Into Helicobacter Pylori Nikr Activation.
Authors: Bahlawane, C. / Dian, C. / Muller, C. / Round, A. / Fauquant, C. / Schauer, K. / De Reuse, H. / Terradot, L. / Michaud-Soret, I.
History
DepositionOct 16, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 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 / struct_site
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 / _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: PUTATIVE NICKEL-RESPONSIVE REGULATOR
B: PUTATIVE NICKEL-RESPONSIVE REGULATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,01617
Polymers34,0162
Non-polymers1,00015
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-82.1 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.534, 70.534, 226.188
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-2022-

HOH

21A-2044-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PUTATIVE NICKEL-RESPONSIVE REGULATOR / HPNIKR


Mass: 17008.080 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Strain: 26695 / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O25896

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Non-polymers , 5 types, 189 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, HIS 74 TO GLY ENGINEERED RESIDUE IN CHAIN A, HIS 75 TO GLY ...ENGINEERED RESIDUE IN CHAIN A, HIS 74 TO GLY ENGINEERED RESIDUE IN CHAIN A, HIS 75 TO GLY ENGINEERED RESIDUE IN CHAIN B, HIS 74 TO GLY ENGINEERED RESIDUE IN CHAIN B, HIS 75 TO GLY

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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: 2.44 Å3/Da / Density % sol: 49.6 % / Description: NONE
Crystal growDetails: 0.4 TO 0.7 M AMMONIUM SULFATE AND 100 MM CITRATE PH 5-5.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9725
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9725 Å / Relative weight: 1
ReflectionResolution: 1.6→61.08 Å / Num. obs: 44866 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 7.6 % / Biso Wilson estimate: 21.15 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.5
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.5 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CAD

2cad


Resolution: 1.6→32.081 Å / SU ML: 0.07 / σ(F): 0.85 / Phase error: 18.37 / Stereochemistry target values: ML
Details: REFINED USING FOBS+ AND FOBS-, NOT FOBS TO VERIFY THE PRESENCE OF METAL IONS.
RfactorNum. reflection% reflection
Rfree0.1995 4162 5.1 %
Rwork0.1847 --
obs0.1854 82300 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 75.022 Å2 / ksol: 0.43 e/Å3
Displacement parametersBiso mean: 32.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.8057 Å20 Å2-0 Å2
2--0.8057 Å20 Å2
3----1.6114 Å2
Refinement stepCycle: LAST / Resolution: 1.6→32.081 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2146 0 57 174 2377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052256
X-RAY DIFFRACTIONf_angle_d0.9983032
X-RAY DIFFRACTIONf_dihedral_angle_d17.91842
X-RAY DIFFRACTIONf_chiral_restr0.082349
X-RAY DIFFRACTIONf_plane_restr0.004389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.65720.26773690.27657609X-RAY DIFFRACTION97
1.6572-1.72350.26194300.23077903X-RAY DIFFRACTION100
1.7235-1.8020.22764220.20987867X-RAY DIFFRACTION100
1.802-1.8970.2024250.19377867X-RAY DIFFRACTION100
1.897-2.01580.2134350.17977858X-RAY DIFFRACTION100
2.0158-2.17140.17364340.16827871X-RAY DIFFRACTION100
2.1714-2.38990.21143990.17127889X-RAY DIFFRACTION100
2.3899-2.73550.19853870.17947882X-RAY DIFFRACTION100
2.7355-3.44580.18594460.16957810X-RAY DIFFRACTION99
3.4458-32.0870.18574150.17897582X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.16911.0865-0.24550.2163-0.10880.41120.1530.08830.22440.0984-0.10540.2536-0.0675-0.1305-0.03930.1228-0.04170.03850.0654-0.01050.137932.209431.7162-3.9015
20.22390.18630.10960.59630.24431.3473-0.04870.0029-0.0219-0.07060.0367-0.0084-0.13580.05110.0260.1277-0.008-0.00240.03640.00020.090228.8669.0878-3.7485
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN 'A' OR CHAIN 'B') AND (RESSEQ 9:63)
2X-RAY DIFFRACTION2(CHAIN 'A' OR CHAIN 'B') AND (RESSEQ 64:147)

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