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- PDB-2ca9: apo-NIKR from helicobacter pylori in closed trans-conformation -

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Basic information

Entry
Database: PDB / ID: 2ca9
Titleapo-NIKR from helicobacter pylori in closed trans-conformation
ComponentsPUTATIVE NICKEL-RESPONSIVE REGULATOR
KeywordsTRANSCRIPTION / NICKEL UPTAKE / TRANSCRIPTION REGULATOR / RIBBON-HELIX-HELIX / ACIDIC-ADAPTIVE RESPONSE / TRANSCRIPTIONAL REGULATION / DNA-BINDING / METAL-BINDING
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 / Putative nickel-responsive regulator
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsDian, C. / Schauer, K. / Kapp, U. / McSweeney, S.M. / Labigne, A. / Terradot, L.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural Basis of the Nickel Response in Helicobacter Pylori: Crystal Structures of Hpnikr in Apo and Nickel-Bound States.
Authors: Dian, C. / Schauer, K. / Kapp, U. / Mcsweeney, S.M. / Labigne, A. / Terradot, L.
History
DepositionDec 20, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2006Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2May 1, 2024Group: 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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)34,93912
Polymers34,3412
Non-polymers59810
Water2,288127
1
A: PUTATIVE NICKEL-RESPONSIVE REGULATOR
B: PUTATIVE NICKEL-RESPONSIVE REGULATOR
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)69,87824
Polymers68,6814
Non-polymers1,19720
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area18050 Å2
ΔGint-92.7 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.055, 71.055, 229.023
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-1148-

FMT

21A-2030-

HOH

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Components

#1: Protein PUTATIVE NICKEL-RESPONSIVE REGULATOR


Mass: 17170.271 Da / Num. of mol.: 2
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 / References: UniProt: O25896
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTRANSCRIPTIONAL REGULATOR.
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 49.1 %
Crystal growpH: 4.8 / Details: 0.9-1 M NA-FORMATE, O.1 M NA-CITRATE PH 4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.05→61.55 Å / Num. obs: 24159 / % possible obs: 99.6 % / Redundancy: 5.4 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.7 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NIKR FROM HELICOBACTER PYLORI SOLVED BY SAD METHOD USING MERCURY DERIVATIVE.

Resolution: 2.05→61.55 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.909 / SU B: 4.171 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1140 5.1 %RANDOM
Rwork0.199 ---
obs0.201 21171 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.05→61.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2171 0 39 127 2337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0212344
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.9383161
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9135292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.21524.444126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.51715429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5451518
X-RAY DIFFRACTIONr_chiral_restr0.1340.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021774
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.21023
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21587
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2160
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.269
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3430.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5181.51469
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.33822277
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.343965
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.1634.5880
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.286 85
Rwork0.222 1517

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