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- PDB-1on1: Bacillus Subtilis Manganese Transport Regulator (Mntr) Bound To M... -

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Basic information

Entry
Database: PDB / ID: 1on1
TitleBacillus Subtilis Manganese Transport Regulator (Mntr) Bound To Manganese, AB Conformation.
ComponentsTranscriptional regulator mntR
KeywordsTRANSCRIPTION / Helix-turn-helix / DNA-Binding Protein / Metalloregulatory Protein
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 ...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
: / HTH-type transcriptional regulator MntR
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsGlasfeld, A. / Guedon, E. / Helmann, J.D. / Brennan, R.G.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Structure of the Manganese-Bound Manganese Transport Regulator of Bacillus subtilis
Authors: Glasfeld, A. / Guedon, E. / Helmann, J.D. / Brennan, R.G.
History
DepositionFeb 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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
Remark 999Authors informed that the individuals who originally sequenced the gene have submitted a revised ...Authors informed that the individuals who originally sequenced the gene have submitted a revised sequence to GenBank which identifies Glu as the correct residue at position 81. The corrected sequence has not yet been published.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator mntR
B: Transcriptional regulator mntR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7946
Polymers33,5742
Non-polymers2204
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-41 kcal/mol
Surface area14060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.120, 46.020, 73.560
Angle α, β, γ (deg.)90.00, 92.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Transcriptional regulator mntR / Manganese transport regulator


Mass: 16787.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pHB7506 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: P54512
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.52 Å3/Da / Density % sol: 51.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 400, 0.15 M Lithium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
20.1 MTris-HCl1reservoirpH8.5
320-30 %(v/v)PEG4001reservoir
40.15 M1reservoirLi2SO4
52 mM1reservoirMnSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.98397 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98397 Å / Relative weight: 1
ReflectionResolution: 1.75→40.5 Å / Num. obs: 32650 / % possible obs: 96.3 % / Observed criterion σ(I): 2.1 / Rmerge(I) obs: 0.048 / Net I/σ(I): 8.5
Reflection shellResolution: 1.75→1.8 Å / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 2.1 / % possible all: 90.7
Reflection
*PLUS
Num. measured all: 107792
Reflection shell
*PLUS
% possible obs: 90.7 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BI2

1bi2


Resolution: 1.75→40.5 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1648 -random
Rwork0.216 ---
obs-32638 96.3 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.998 Å20 Å22.967 Å2
2--3.731 Å20 Å2
3---3.267 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.75→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2130 0 4 370 2504
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg0.98
X-RAY DIFFRACTIONc_bond_d0.0044
X-RAY DIFFRACTIONc_mcbond_it1.5011.5
X-RAY DIFFRACTIONc_scbond_it2.4552
X-RAY DIFFRACTIONc_mcangle_it2.3662
X-RAY DIFFRACTIONc_scangle_it3.7962.5
LS refinement shellResolution: 1.75→1.81 Å
RfactorNum. reflection% reflection
Rfree0.379 125 -
Rwork0.325 --
obs-2970 91.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.004

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