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

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Basic information

Entry
Database: PDB / ID: 2wve
TitleStructural and mechanistic insights into Helicobacter pylori NikR function
ComponentsPUTATIVE NICKEL-RESPONSIVE REGULATOR
KeywordsTRANSCRIPTION / TRANSCRIPTION FACTOR / TRANSCRIPTION REGULATION / RHH / 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 / Arc-type ribbon-helix-helix ...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
CITRIC ACID / Putative nickel-responsive regulator
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 / 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 / _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)35,44912
Polymers34,3792
Non-polymers1,07110
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-89.9 kcal/mol
Surface area13350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.761, 118.761, 50.294
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PUTATIVE NICKEL-RESPONSIVE REGULATOR / HPNIKR


Mass: 17189.316 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, 104 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, GLN 87 TO PHE ENGINEERED RESIDUE IN CHAIN B, GLN 87 TO PHE

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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: 2.66 Å3/Da / Density % sol: 53.84 % / Description: NONE
Crystal growDetails: 0.4-0.7 M AMMONIUM SULFATE, 100 MM CITRATE PH 5-5.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→46.32 Å / Num. obs: 16561 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 14.8 % / Biso Wilson estimate: 32.86 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 15.3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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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 2CA9

2ca9


Resolution: 2.3→46.312 Å / SU ML: 0.37 / σ(F): 1.41 / Phase error: 17.65 / Stereochemistry target values: ML
Details: THE STRUCTURE WAS REFINED USING FOBS+ AND FOBS- AND NOT FOBS TO VERIFY THE PRESENCE OF METAL IONS
RfactorNum. reflection% reflection
Rfree0.2039 1541 5.1 %
Rwork0.1954 --
obs0.1959 30527 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.102 Å2 / ksol: 0.398 e/Å3
Displacement parametersBiso mean: 43.38 Å2
Baniso -1Baniso -2Baniso -3
1-1.9484 Å20 Å2-0 Å2
2--1.9484 Å20 Å2
3----3.8968 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.312 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2110 0 64 94 2268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032192
X-RAY DIFFRACTIONf_angle_d0.6932954
X-RAY DIFFRACTIONf_dihedral_angle_d18.836807
X-RAY DIFFRACTIONf_chiral_restr0.05336
X-RAY DIFFRACTIONf_plane_restr0.002376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.38230.21841840.21582885X-RAY DIFFRACTION100
2.3823-2.47770.1991450.21382906X-RAY DIFFRACTION100
2.4777-2.59050.22522000.21922839X-RAY DIFFRACTION100
2.5905-2.7270.24341270.21342923X-RAY DIFFRACTION100
2.727-2.89790.19821770.21562871X-RAY DIFFRACTION100
2.8979-3.12160.20621600.20562912X-RAY DIFFRACTION100
3.1216-3.43560.20031310.1892905X-RAY DIFFRACTION100
3.4356-3.93250.19561450.16842907X-RAY DIFFRACTION100
3.9325-4.95370.16441440.16512918X-RAY DIFFRACTION100
4.9537-46.32160.21551280.21152920X-RAY DIFFRACTION100
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)
10.32460.11890.1542.85140.45631.8417-0.01160.04370.110.13790.05140.21390.114-0.1546-0.04650.05880.0111-0.00040.1031-0.00990.068245.60214.5822.8025
21.1935-0.9630.34611.68560.27020.61420.0940.0366-0.0855-0.1569-0.08770.0757-0.0619-0.01870.02860.12810.0272-0.00170.1023-0.00420.102229.761322.81428.4424
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 64:143)

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