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- PDB-2y3y: Holo-Ni(II) HpNikR is a symmetric tetramer containing four canoni... -

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Basic information

Entry
Database: PDB / ID: 2y3y
TitleHolo-Ni(II) HpNikR is a symmetric tetramer containing four canonic square-planar Ni(II) ions at physiological pH
Components
  • PUTATIVE NICKEL-RESPONSIVE REGULATOR
  • UNDECAPEPTIDE-GSSSGSASGAG
KeywordsTRANSCRIPTION / METAL BINDING
Function / homology
Function and homology information


response to nickel cation / DNA-binding transcription repressor activity / nickel cation binding / protein-DNA complex / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription
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 / Arc-type ribbon-helix-helix / 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 / Arc-type ribbon-helix-helix / Ribbon-helix-helix / ACT-like domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / Putative nickel-responsive regulator
Similarity search - Component
Biological speciesHELICOBACTER PYLORI G27 (bacteria)
UNIDENTIFIED (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.39 Å
AuthorsBenini, S. / Cianci, M. / Ciurli, S.
CitationJournal: Dalton Trans / Year: 2011
Title: Holo-Ni(2+)Helicobacter Pylori Nikr Contains Four Square-Planar Nickel-Binding Sites at Physiological Ph.
Authors: Benini, S. / Cianci, M. / Ciurli, S.
History
DepositionJan 4, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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.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.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.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_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
Q: UNDECAPEPTIDE-GSSSGSASGAG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,56914
Polymers42,5395
Non-polymers1,0309
Water1,18966
1
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)42,74513
Polymers41,7154
Non-polymers1,0309
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-95.5 kcal/mol
Surface area15220 Å2
MethodPISA
2
Q: UNDECAPEPTIDE-GSSSGSASGAG


Theoretical massNumber of molelcules
Total (without water)8241
Polymers8241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.970, 72.970, 116.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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Protein / Protein/peptide , 2 types, 5 molecules ABCDQ

#1: Protein
PUTATIVE NICKEL-RESPONSIVE REGULATOR / HOLO-NICKEL HPNIKR


Mass: 10428.796 Da / Num. of mol.: 4 / Fragment: C-TERMINAL METAL-BINDING DOMAIN, RESIDUES 58-145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI G27 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B5Z8Y5
#2: Protein/peptide UNDECAPEPTIDE-GSSSGSASGAG


Mass: 823.767 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) UNIDENTIFIED (others)

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Non-polymers , 4 types, 75 molecules

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


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsONLY C-TERMINAL METAL-BINDING DOMAIN PRESENT.

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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: 4.05 Å3/Da / Density % sol: 69.64 % / Description: NONE
Crystal growpH: 7.3 / Details: 20% PEG 3350 AND 0.2 M K/NA-TARTRATE, pH 7.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.459
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 2.39→19.94 Å / Num. obs: 24202 / % possible obs: 99.8 % / Observed criterion σ(I): 3.5 / Redundancy: 14 % / Biso Wilson estimate: 52.396 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 26.8
Reflection shellResolution: 2.39→2.52 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.39→72.98 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.885 / SU B: 6.966 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.294 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. UNEXPECTED ELECTRON DENSITY WAS MODELED AS ALPHA-CHAIN (Q)
RfactorNum. reflection% reflectionSelection details
Rfree0.27892 1177 5.1 %RANDOM
Rwork0.22917 ---
obs0.2317 21766 94.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.377 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2---0.26 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.39→72.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2686 0 55 66 2807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0212773
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2161.9453720
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6675336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.88324.706136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.57215516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7791516
X-RAY DIFFRACTIONr_chiral_restr0.1630.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022000
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4961.51673
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.80322696
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.96631100
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.4284.51024
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: 2.39→2.452 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 78 -
Rwork0.25 1485 -
obs--87.56 %

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