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

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Basic information

Entry
Database: PDB / ID: 2wvd
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 ...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 speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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
C: PUTATIVE NICKEL-RESPONSIVE REGULATOR
D: PUTATIVE NICKEL-RESPONSIVE REGULATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,74616
Polymers68,6174
Non-polymers1,12912
Water1,06359
1
C: PUTATIVE NICKEL-RESPONSIVE REGULATOR
D: PUTATIVE NICKEL-RESPONSIVE REGULATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9659
Polymers34,3082
Non-polymers6577
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-75.1 kcal/mol
Surface area13300 Å2
MethodPISA
2
A: PUTATIVE NICKEL-RESPONSIVE REGULATOR
B: PUTATIVE NICKEL-RESPONSIVE REGULATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7817
Polymers34,3082
Non-polymers4725
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-76.7 kcal/mol
Surface area13410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.970, 116.980, 123.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
PUTATIVE NICKEL-RESPONSIVE REGULATOR / HPNIKR


Mass: 17154.205 Da / Num. of mol.: 4 / 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
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 96 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 96 TO SER ...ENGINEERED RESIDUE IN CHAIN A, CYS 96 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 96 TO SER ENGINEERED RESIDUE IN CHAIN C, CYS 96 TO SER ENGINEERED RESIDUE IN CHAIN D, CYS 96 TO SER

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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: 2.72 Å3/Da / Density % sol: 54.8 % / 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: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 28, 2009
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.65→46.32 Å / Num. obs: 21767 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Biso Wilson estimate: 48.78 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.1
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CA9

2ca9


Resolution: 2.65→38.958 Å / SU ML: 0.84 / σ(F): 1.18 / Phase error: 21.87 / 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
Rfree0.2308 2081 5.1 %
Rwork0.2051 --
obs0.2064 40515 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.295 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso mean: 52.49 Å2
Baniso -1Baniso -2Baniso -3
1--7.5169 Å20 Å20 Å2
2--1.5028 Å2-0 Å2
3---6.0142 Å2
Refinement stepCycle: LAST / Resolution: 2.65→38.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4261 0 66 59 4386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034368
X-RAY DIFFRACTIONf_angle_d0.7825881
X-RAY DIFFRACTIONf_dihedral_angle_d18.6591606
X-RAY DIFFRACTIONf_chiral_restr0.06683
X-RAY DIFFRACTIONf_plane_restr0.002751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6501-2.74480.3142180.28943848X-RAY DIFFRACTION100
2.7448-2.85470.27081830.26063860X-RAY DIFFRACTION100
2.8547-2.98450.28922240.25493861X-RAY DIFFRACTION100
2.9845-3.14180.27332380.23923828X-RAY DIFFRACTION100
3.1418-3.33860.25211950.22783905X-RAY DIFFRACTION100
3.3386-3.59620.21782300.1883821X-RAY DIFFRACTION100
3.5962-3.95780.21551690.17963883X-RAY DIFFRACTION100
3.9578-4.52970.18931960.15773875X-RAY DIFFRACTION99
4.5297-5.70410.18752120.17663776X-RAY DIFFRACTION99
5.7041-38.96230.2282160.21313777X-RAY DIFFRACTION98
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)
12.22740.48640.13153.117-0.62231.70880.054-0.28080.14470.20210.11430.1664-0.0433-0.108-00.1927-0.0107-0.01010.19750.01020.1311-29.037615.0133-48.6571
20.79350.8386-0.46732.2701-0.92471.798-0.0556-0.02680.0110.0446-0.0254-0.097-0.03890.044300.12480.0381-0.0360.16930.04560.2025-14.92596.9152-32.4653
31.6680.18120.09660.62350.2232.29040.0429-0.08170.0894-0.0466-0.09690.0087-0.10950.0245-00.19220.0072-0.00070.14110.02960.160416.1528-15.8488-15.5146
41.14460.1902-0.45381.3414-0.36761.18690.01070.0338-0.04840.01830.06140.0005-0.0486-0.095300.20390.0349-0.02680.26140.04810.23032.087-1.7498-26.1187
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A OR CHAIN B) AND RESSEQ 6:63
2X-RAY DIFFRACTION2(CHAIN A OR CHAIN B) AND RESSEQ 64:143
3X-RAY DIFFRACTION3(CHAIN C OR CHAIN D) AND RESSEQ 8:63
4X-RAY DIFFRACTION4(CHAIN C OR CHAIN D) AND RESSEQ 64:145

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