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- PDB-3pht: Crystal structure of H74A mutant of Helicobacter Pylori NikR -

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Basic information

Entry
Database: PDB / ID: 3pht
TitleCrystal structure of H74A mutant of Helicobacter Pylori NikR
ComponentsPutative nickel-responsive regulator
KeywordsTRANSCRIPTION / Transcription factor
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 / 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 / Putative nickel-responsive regulator
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsPozharski, E. / Evans, S. / Michel, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Ni(II) coordination to mixed sites modulates DNA binding of HpNikR via a long-range effect.
Authors: West, A.L. / Evans, S.E. / Gonzalez, J.M. / Carter, L.G. / Tsuruta, H. / Pozharski, E. / Michel, S.L.
History
DepositionNov 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Apr 25, 2012Group: Database references
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_ref_seq_dif.details / _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

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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)34,3244
Polymers34,2062
Non-polymers1172
Water1,71195
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)68,6488
Polymers68,4134
Non-polymers2354
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8790 Å2
ΔGint-98 kcal/mol
Surface area17480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.174, 73.174, 114.441
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Putative nickel-responsive regulator


Mass: 17103.201 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: HP_1338 / Production host: Escherichia coli (E. coli) / References: UniProt: O25896
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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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: 2.24 Å3/Da / Density % sol: 45.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12% PEG20K, 0.1M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 27, 2010 / Details: mirrors
RadiationMonochromator: OSMIC mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.04→61.65 Å / Num. all: 20487 / Num. obs: 20487 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 24.3 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 25.8
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 22.1 % / Mean I/σ(I) obs: 1.1 / Num. unique all: 1997 / % possible all: 100

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.6.0077refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LGH, residues 60-140

3lgh


Resolution: 2.04→61.65 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.489 / SU ML: 0.093 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22999 1038 5.1 %RANDOM
Rwork0.19084 ---
all0.19267 19253 --
obs0.19267 19253 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.868 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2---0.29 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.04→61.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1535 0 2 95 1632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0211656
X-RAY DIFFRACTIONr_angle_refined_deg2.0931.9332263
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6075226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.94524.70685
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.42115304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4281512
X-RAY DIFFRACTIONr_chiral_restr0.1760.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021255
LS refinement shellResolution: 2.041→2.094 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.504 75 -
Rwork0.538 1383 -
obs--98.58 %
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)
13.03740.6385-1.61112.5251-0.43532.01010.03320.0640.2408-0.0648-0.09460.4306-0.0436-0.71630.06140.06280.0251-0.01690.4266-0.09530.25792.42420.7275.184
23.68710.51310.1031.30720.63572.1464-0.058-0.2510.06410.0627-0.1680.27180.0818-0.40130.22610.0723-0.0150.01360.205-0.04780.17034.47717.4988.697
31.90250.0761-0.90163.190.03854.61890.02370.1025-0.0203-0.3959-0.05710.1455-0.343-0.43340.03340.1680.0476-0.03620.0843-0.00620.125810.6422.252-8.637
45.27762.18282.35951.44041.36428.4797-0.04480.07230.3083-0.39130.03360.4929-0.838-1.05630.01120.53080.1631-0.10.3040.00640.44145.7228.491-9.014
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 89
2X-RAY DIFFRACTION2A90 - 144
3X-RAY DIFFRACTION3B60 - 120
4X-RAY DIFFRACTION4B121 - 141

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