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- PDB-6mrj: Crystal structure of H.pylori NikR in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 6mrj
TitleCrystal structure of H.pylori NikR in complex with DNA
Components
  • (DNA (36-MER)) x 2
  • Nickel-responsive regulator
KeywordsDNA BINDING PROTEIN/DNA / nickel / protein-DNA complex / transcription factor / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
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
NICKEL (II) ION / DNA / DNA (> 10) / Putative nickel-responsive regulator
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPozharski, E. / de Serrano, V.
CitationJournal: To Be Published
Title: Crystal structure of H.pylori NikR in complex with DNA
Authors: Pozharski, E. / de Serrano, V.
History
DepositionOct 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nickel-responsive regulator
B: Nickel-responsive regulator
C: Nickel-responsive regulator
D: Nickel-responsive regulator
L: DNA (36-MER)
M: DNA (36-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,10712
Polymers90,8236
Non-polymers2836
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24920 Å2
ΔGint-213 kcal/mol
Surface area32120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.370, 94.180, 204.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Nickel-responsive regulator


Mass: 17170.271 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / Gene: HP_1338 / Production host: Escherichia coli (E. coli) / References: UniProt: O25896

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DNA chain , 2 types, 2 molecules LM

#2: DNA chain DNA (36-MER)


Mass: 11133.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (36-MER)


Mass: 11009.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 41 molecules

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


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 4.02 Å3/Da / Density % sol: 72.7 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG 3350, 0.2M NaF, 20mM HEPES pH 8.0, 0.1M NaCl, 10mM Mg2Cl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→39.49 Å / Num. obs: 35339 / % possible obs: 100 % / Redundancy: 123.2 % / Biso Wilson estimate: 79.37 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.192 / Net I/σ(I): 10.9
Reflection shellResolution: 2.8→2.93 Å / Redundancy: 120.7 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 4619 / CC1/2: 0.38 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LGH

3lgh


Resolution: 2.8→39.47 Å / Cor.coef. Fo:Fc: 0.9263 / Cor.coef. Fo:Fc free: 0.9043 / SU R Cruickshank DPI: 0.424 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.433 / SU Rfree Blow DPI: 0.276 / SU Rfree Cruickshank DPI: 0.277
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 1721 4.89 %RANDOM
Rwork0.2072 ---
obs0.2088 35178 100 %-
Displacement parametersBiso mean: 100.23 Å2
Baniso -1Baniso -2Baniso -3
1-15.9129 Å20 Å20 Å2
2---34.3121 Å20 Å2
3---18.3991 Å2
Refine analyzeLuzzati coordinate error obs: 0.501 Å
Refinement stepCycle: 1 / Resolution: 2.8→39.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4513 1470 6 35 6024
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0096226HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.058722HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2059SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes160HARMONIC2
X-RAY DIFFRACTIONt_gen_planes725HARMONIC5
X-RAY DIFFRACTIONt_it6226HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.47
X-RAY DIFFRACTIONt_other_torsion21.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion828SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6662SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.88 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2983 141 4.93 %
Rwork0.2589 2717 -
all0.2608 2858 -
obs--100 %

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