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- PDB-2hyg: The Structure of apo-MntR from Bacillus subtilis, Native Form -

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Basic information

Entry
Database: PDB / ID: 2hyg
TitleThe Structure of apo-MntR from Bacillus subtilis, Native Form
ComponentsTranscriptional regulator mntR
KeywordsTRANSCRIPTION / transcriptional regulator
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
HTH-type transcriptional regulator MntR
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGlasfeld, A. / Kliegman, J.I.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The conformations of the manganese transport regulator of Bacillus subtilis in its metal-free state.
Authors: DeWitt, M.A. / Kliegman, J.I. / Helmann, J.D. / Brennan, R.G. / Farrens, D.L. / Glasfeld, A.
History
DepositionAug 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE THE AUTHORS STATE THAT THE UNP SEQUENCE HAS AN ERROR AT RESIDUE 81. THE TRUE RESIDUE IS ...SEQUENCE THE AUTHORS STATE THAT THE UNP SEQUENCE HAS AN ERROR AT RESIDUE 81. THE TRUE RESIDUE IS GLUTAMATE, AS IS FOUND IN THEIR STRUCTURE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Transcriptional regulator mntR


Theoretical massNumber of molelcules
Total (without water)16,7871
Polymers16,7871
Non-polymers00
Water181
1
D: Transcriptional regulator mntR

D: Transcriptional regulator mntR


Theoretical massNumber of molelcules
Total (without water)33,5742
Polymers33,5742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_795x-y+2,-y+4,-z+2/31
Unit cell
Length a, b, c (Å)42.000, 42.000, 149.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe second part of the biological assembly is generated by the two fold axis: x-y+1, -y+3, 2/3-y

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Components

#1: Protein Transcriptional regulator mntR / Manganese transport regulator


Mass: 16787.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: P54512
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG 4000, 0.2 M ammonium sulfate, 5 mM cobalt(II) chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2.8→74.5 Å / Num. obs: 4162 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 13.2 % / Biso Wilson estimate: 104 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 8.8
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HYF, chain D

2hyf


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.894 / SU B: 54.706 / SU ML: 0.502 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.542 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.34206 423 10.3 %RANDOM
Rwork0.27353 ---
obs0.28016 3695 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 97.859 Å2
Baniso -1Baniso -2Baniso -3
1-2.39 Å21.19 Å20 Å2
2--2.39 Å20 Å2
3----3.58 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1102 0 0 1 1103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221120
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0921.9791503
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0235132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93724.64356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.22115227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.947157
X-RAY DIFFRACTIONr_chiral_restr0.070.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02823
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.2514
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2791
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.227
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2980.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3281.5685
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.57921066
X-RAY DIFFRACTIONr_scbond_it0.8353498
X-RAY DIFFRACTIONr_scangle_it1.4144.5437
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.535 33 -
Rwork0.279 237 -
obs--99.26 %
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)
16.418-0.25212.45077.91761.79649.70380.37040.0117-0.2864-0.0091-0.53730.72930.0407-1.02050.16680.28540.33890.1661-0.20680.1196-0.1463-28.075682.032429.7815
26.19781.75390.38167.0480.23737.55650.85520.0134-0.2569-0.2968-0.4829-0.7298-0.32910.3942-0.37230.35340.12860.1676-0.40890.1521-0.3611-10.219975.05743.3319
318.0091-2.3004-6.3948.7281-9.87564.6275-1.37611.1855-1.7460.93940.6047-1.39-0.12881.81260.77140.45030.1928-0.31890.5452-0.08760.30563.53864.070646.2309
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1DA3 - 723 - 72
2X-RAY DIFFRACTION2DA73 - 12573 - 125
3X-RAY DIFFRACTION3DA126 - 135126 - 135

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