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- PDB-4hx8: Structure of metal-free MNTR mutant E11K -

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Basic information

Entry
Database: PDB / ID: 4hx8
TitleStructure of metal-free MNTR mutant E11K
ComponentsTranscriptional regulator MntR
KeywordsTRANSCRIPTION / WINGED HELIX-TURN-HELIX / TRANSCRIPTION 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 ...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 subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / EPmolecular replacement / Resolution: 2.001 Å
AuthorsGlasfeld, A. / Mcguire, A.
CitationJournal: Biochemistry / Year: 2013
Title: Roles of the A and C Sites in the Manganese-Specific Activation of MntR.
Authors: McGuire, A.M. / Cuthbert, B.J. / Ma, Z. / Grauer-Gray, K.D. / Brunjes Brophy, M. / Spear, K.A. / Soonsanga, S. / Kliegman, J.I. / Griner, S.L. / Helmann, J.D. / Glasfeld, A.
History
DepositionNov 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator MntR
B: Transcriptional regulator MntR


Theoretical massNumber of molelcules
Total (without water)33,3122
Polymers33,3122
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-16 kcal/mol
Surface area14520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.920, 86.710, 91.190
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 Transcriptional regulator MntR / Manganese transport regulator


Mass: 16656.000 Da / Num. of mol.: 2 / Mutation: E11K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: mntR, yqhN, BSU24520 / Production host: Escherichia coli (E. coli) / References: UniProt: P54512
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 5% PEG 4000, 4% ethanol, 2% 1,4-butanediol, 4 mM EDTA, 0.1 M sodium acetate , pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2010
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2→45.6 Å / Num. obs: 21377 / % possible obs: 99.2 % / Redundancy: 6.5 % / Net I/σ(I): 17.4
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 5.7 / % possible all: 94.5

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Processing

Software
NameVersionClassification
BALBESphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: EPmolecular replacement
Starting model: 2HYF

2hyf


Resolution: 2.001→43.355 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 29.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2994 1086 5.1 %RANDOM
Rwork0.2354 ---
obs0.2386 21289 98.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.873 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.0296 Å2-0 Å2-0 Å2
2---1.4684 Å20 Å2
3----1.5612 Å2
Refinement stepCycle: LAST / Resolution: 2.001→43.355 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2169 0 0 51 2220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082223
X-RAY DIFFRACTIONf_angle_d1.0062979
X-RAY DIFFRACTIONf_dihedral_angle_d15.714878
X-RAY DIFFRACTIONf_chiral_restr0.067325
X-RAY DIFFRACTIONf_plane_restr0.003374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.001-2.09210.38991400.3062430X-RAY DIFFRACTION97
2.0921-2.20240.3511230.29082488X-RAY DIFFRACTION99
2.2024-2.34040.34461490.26342489X-RAY DIFFRACTION99
2.3404-2.5210.32361400.25452495X-RAY DIFFRACTION100
2.521-2.77470.32661560.25282533X-RAY DIFFRACTION100
2.7747-3.17610.34711300.24942529X-RAY DIFFRACTION100
3.1761-4.00110.2621280.22282597X-RAY DIFFRACTION100
4.0011-43.36520.24671200.20172642X-RAY DIFFRACTION97
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)
15.1440.2054-0.79033.4174-3.61334.21321.26650.1852-0.41470.2914-0.74130.00830.15610.8941-0.19360.40670.0172-0.19630.30750.00530.204617.012166.496438.8534
27.86410.60731.60052.45594.74239.9723-0.04860.7569-0.5838-0.0031.5897-0.8554-0.38992.595-1.34580.10920.04070.02360.7426-0.21420.300825.251867.829332.267
31.5840.5161-1.54971.4345-2.18598.09070.52910.17470.0951-0.1889-0.07420.0489-0.69561.1117-0.38910.25830.02660.01660.2994-0.07340.19113.75270.711127.7892
42.87621.12563.14850.5451.62766.56990.8029-0.8463-0.30270.7194-0.28580.00612.5546-1.0593-0.4080.8912-0.2647-0.07480.16690.0910.21379.94559.083239.1697
54.3096-2.2763-3.16356.1961.43852.35330.58780.11840.6474-2.25430.1117-0.5154-0.909-0.0118-0.44350.7887-0.16390.09580.0588-0.03150.122321.346850.361350.0136
60.9171-0.1251-0.18197.28852.05990.6128-0.1982-0.1722-0.1155-0.29830.27620.5478-0.5514-0.00380.05130.4097-0.014-0.11220.18510.01940.160211.264345.422357.5947
74.30441.75860.10283.03350.12420.08970.1362-1.23950.1325-0.045-0.28180.2654-0.0348-0.02590.1140.13-0.02280.01940.4357-0.02830.12328.559523.725336.8829
85.2821-1.2792-2.89311.4030.56631.77010.0747-0.60830.6384-0.33810.2952-0.0721-0.21530.6788-0.37090.1304-0.1287-0.03090.4094-0.03950.165436.965426.041432.9313
99.3812-1.4738-5.73331.96962.355.2627-0.0563-3.34420.40780.180.7277-0.2046-0.12611.8758-0.72540.0442-0.0370.01861.0282-0.18050.11430.127626.635147.1753
100.9772-0.0063-0.1368.8960.83510.1038-0.06090.0869-0.1462-2.25820.36340.3955-0.35490.1066-0.22840.5802-0.1669-0.05750.1865-0.05360.135814.211835.906844.0053
115.49924.37080.96155.12592.39212.3076-0.22840.7588-0.1625-0.38860.7235-0.5079-0.16560.0603-0.34420.1954-0.0396-0.04180.252-0.07640.201622.952239.416752.9914
122.4962-3.22040.56344.7719-1.65012.03330.2108-0.202-0.55920.18870.0121.1256-0.5787-0.1275-0.27750.3306-0.03130.01020.11090.04860.38284.371838.360557.4236
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 5:24)
2X-RAY DIFFRACTION2(chain A and resid 25:43)
3X-RAY DIFFRACTION3(chain A and resid 44:62)
4X-RAY DIFFRACTION4(chain A and resid 63:77)
5X-RAY DIFFRACTION5(chain A and resid 78:105)
6X-RAY DIFFRACTION6(chain A and resid 106:136)
7X-RAY DIFFRACTION7(chain B and resid 4:29)
8X-RAY DIFFRACTION8(chain B and resid 30:60)
9X-RAY DIFFRACTION9(chain B and resid 61:78)
10X-RAY DIFFRACTION10(chain B and resid 79:102)
11X-RAY DIFFRACTION11(chain B and resid 103:118)
12X-RAY DIFFRACTION12(chain B and resid 119:136)

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