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- PDB-2hyf: The Structure of apo-MntR from Bacillus subtilis, selenomethionin... -

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Basic information

Entry
Database: PDB / ID: 2hyf
TitleThe Structure of apo-MntR from Bacillus subtilis, selenomethionine derivative
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 / MAD / Resolution: 2.8 Å
AuthorsGlasfeld, A.
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: Version format compliance
Remark 999 SEQUENCE 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,00214
Polymers67,8994
Non-polymers1,10310
Water39622
1
A: Transcriptional regulator mntR
B: Transcriptional regulator mntR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3346
Polymers33,9492
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-67 kcal/mol
Surface area14420 Å2
MethodPISA
2
C: Transcriptional regulator mntR
D: Transcriptional regulator mntR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6688
Polymers33,9492
Non-polymers7196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-76 kcal/mol
Surface area15290 Å2
MethodPISA
3
D: Transcriptional regulator mntR
hetero molecules

A: Transcriptional regulator mntR
B: Transcriptional regulator mntR
C: Transcriptional regulator mntR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,00214
Polymers67,8994
Non-polymers1,10310
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
identity operation1_555x,y,z1
Buried area7710 Å2
ΔGint-148 kcal/mol
Surface area28960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.890, 65.030, 186.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTwo copies of the biologically active dimer are present in the asymmetric unit, composed of chains A and B, and chains C and D.

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Components

#1: Protein
Transcriptional regulator mntR / Manganese transport regulator


Mass: 16974.711 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: P54512
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG 400, 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: 8.2.1 / Wavelength: 0.9793,0.9796,0.9641
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 26, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97961
30.96411
ReflectionResolution: 2.8→64.6 Å / Num. obs: 16290 / % possible obs: 93.6 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 6.3
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 2 / % possible all: 79.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.277 1614 RANDOM
Rwork0.217 --
obs-16208 -
Displacement parametersBiso mean: 49.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.837 Å20 Å20 Å2
2---0.325 Å20 Å2
3---4.162 Å2
Refine analyzeLuzzati sigma a obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4423 0 60 22 4505
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2

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