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- PDB-6ktb: Crystal structure of B. halodurans MntR in apo form -

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Basic information

Entry
Database: PDB / ID: 6ktb
TitleCrystal structure of B. halodurans MntR in apo form
ComponentsHTH-type transcriptional regulator MntR
KeywordsTRANSCRIPTION / MntR / transcription factor
Function / homology
Function and homology information


intracellular manganese ion homeostasis / manganese ion binding / protein dimerization activity / DNA-binding transcription factor activity / DNA binding / cytoplasm
Similarity search - Function
HTH-type transcription regulator MntR / Iron dependent repressor, metal binding and dimerisation domain / DtxR-type HTH domain profile. / DTXR-type HTH domain / Iron dependent repressor, N-terminal DNA binding domain / Iron dependent repressor, metal binding and dimerisation domain / Iron dependent repressor / Iron dependent repressor, metal binding and dimerisation domain superfamily / Iron dependent repressor, metal binding and dimerisation domain / Helix-turn-helix diphteria tox regulatory element ...HTH-type transcription regulator MntR / Iron dependent repressor, metal binding and dimerisation domain / DtxR-type HTH domain profile. / DTXR-type HTH domain / Iron dependent repressor, N-terminal DNA binding domain / Iron dependent repressor, metal binding and dimerisation domain / Iron dependent repressor / Iron dependent repressor, metal binding and dimerisation domain superfamily / Iron dependent repressor, metal binding and dimerisation domain / Helix-turn-helix diphteria tox regulatory element / Diphtheria Toxin Repressor; domain 2 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / PHOSPHATE ION / HTH-type transcriptional regulator MntR
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLee, J.Y. / Lee, M.Y.
CitationJournal: Plos One / Year: 2019
Title: Structural analysis of the manganese transport regulator MntR from Bacillus halodurans in apo and manganese bound forms.
Authors: Lee, M.Y. / Lee, D.W. / Joo, H.K. / Jeong, K.H. / Lee, J.Y.
History
DepositionAug 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH-type transcriptional regulator MntR
B: HTH-type transcriptional regulator MntR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1868
Polymers32,7672
Non-polymers4196
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-50 kcal/mol
Surface area15430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.528, 89.370, 109.945
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 HTH-type transcriptional regulator MntR / Manganese transport regulator


Mass: 16383.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125) (bacteria)
Gene: mntR, BH2807 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9K943
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.96 Å3/Da / Density % sol: 58.49 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: sodium phosphate, magensium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 14131 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 14.1
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 7.9

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Processing

Software
NameClassification
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→37.197 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.218 --
Rwork0.171 --
obs-14082 98.57 %
Refinement stepCycle: LAST / Resolution: 2.5→37.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2284 0 18 77 2379

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