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- PDB-9f80: Crystal structure of Rv2242 regulator C-terminal fragment (161-414) -

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Basic information

Entry
Database: PDB / ID: 9f80
TitleCrystal structure of Rv2242 regulator C-terminal fragment (161-414)
ComponentsUncharacterized protein Rv2242
KeywordsTRANSCRIPTION / HELIX-TURN-HELIX / PUCR FAMILY / TUBERCULOSIS / DNA BINDING PROTEIN
Function / homologyPucR C-terminal helix-turn-helix domain / PucR C-terminal helix-turn-helix domain superfamily / : / PucR C-terminal helix-turn-helix domain / CdaR, GGDEF-like domain / GGDEF-like domain / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / Uncharacterized protein Rv2242
Function and homology information
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.027 Å
AuthorsMegalizzi, V. / Tanina, A. / Grosse, C. / Mirgaux, M. / Legrand, P. / Dias Mirandela, G. / Wohlkonig, A. / Bifani, P. / Wintjens, R.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Fonds National de la Recherche Scientifique (FNRS)CR40003580 Belgium
CitationJournal: Heliyon / Year: 2024
Title: Domain architecture of the Mycobacterium tuberculosis MabR ( Rv2242 ), a member of the PucR transcription factor family.
Authors: Megalizzi, V. / Tanina, A. / Grosse, C. / Mirgaux, M. / Legrand, P. / Dias Mirandela, G. / Wohlkonig, A. / Bifani, P. / Wintjens, R.
History
DepositionMay 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein Rv2242
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2523
Polymers29,1071
Non-polymers1452
Water68538
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint4 kcal/mol
Surface area11750 Å2
Unit cell
Length a, b, c (Å)63.040, 75.280, 139.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-624-

HOH

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Components

#1: Protein Uncharacterized protein Rv2242


Mass: 29106.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: Rv2242, MTCY427.23 / Plasmid: plasmid / Details (production host): pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WPH5
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.85 Å3/Da / Density % sol: 56.88 %
Crystal growTemperature: 277 K / Method: slow cooling / pH: 7.5
Details: 20 mM HEPES, pH7.5, 400 mM NaCl, 5% glycerol, 5 mM beta-mercaptoethanol, 400 mM imidazole, temperature 277K, slow cooling

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.027→48.378 Å / Num. obs: 21908 / % possible obs: 99.7 % / Redundancy: 13.4 % / CC1/2: 0.732 / Rrim(I) all: 0.073 / Net I/σ(I): 22.81
Reflection shellResolution: 2.027→2.15 Å / Redundancy: 13.5 % / Num. unique obs: 3440 / CC1/2: 0.681 / Rrim(I) all: 1.353 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDS20190315data reduction
XDS20190315data scaling
SHELXD2016/1phasing
PHASER2.8.3phasing
MOLREP11.7.02phasing
RefinementMethod to determine structure: SAD / Resolution: 2.027→48.378 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.703 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.156
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2543 1096 5.003 %
Rwork0.1964 20812 -
all0.199 --
obs-21908 99.754 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 51.793 Å2
Baniso -1Baniso -2Baniso -3
1-1.995 Å2-0 Å20 Å2
2---0.834 Å2-0 Å2
3----1.161 Å2
Refinement stepCycle: LAST / Resolution: 2.027→48.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 9 38 1834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0121829
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161754
X-RAY DIFFRACTIONr_angle_refined_deg2.2071.6532501
X-RAY DIFFRACTIONr_angle_other_deg0.7031.5774017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1145241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.777519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.09810268
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.1231070
X-RAY DIFFRACTIONr_chiral_restr0.0930.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022212
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02400
X-RAY DIFFRACTIONr_nbd_refined0.2440.2435
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.21601
X-RAY DIFFRACTIONr_nbtor_refined0.1950.2934
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21034
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.266
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.120.212
X-RAY DIFFRACTIONr_nbd_other0.2110.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1340.210
X-RAY DIFFRACTIONr_mcbond_it6.4595.09971
X-RAY DIFFRACTIONr_mcbond_other6.4485.09970
X-RAY DIFFRACTIONr_mcangle_it8.0339.0791209
X-RAY DIFFRACTIONr_mcangle_other8.0459.0841210
X-RAY DIFFRACTIONr_scbond_it7.9765.632858
X-RAY DIFFRACTIONr_scbond_other7.9725.636859
X-RAY DIFFRACTIONr_scangle_it10.510.0311292
X-RAY DIFFRACTIONr_scangle_other10.49610.031293
X-RAY DIFFRACTIONr_lrange_it11.60649.812048
X-RAY DIFFRACTIONr_lrange_other11.65749.8192047
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.027-2.0790.484770.38914530.39415810.8610.91396.77420.386
2.079-2.1360.315790.30215090.30315880.9120.9451000.292
2.136-2.1980.319740.27914090.28114830.9490.9511000.261
2.198-2.2650.327740.2914110.29214860.9220.94899.93270.265
2.265-2.3390.281730.22213760.22514490.9560.971000.195
2.339-2.4210.239680.20312980.20513660.9650.9761000.178
2.421-2.5130.25670.20712720.20913390.9570.9741000.177
2.513-2.6150.333650.22112220.22612870.9280.971000.193
2.615-2.7310.31620.20911970.21412590.9380.9751000.183
2.731-2.8640.294590.19711140.20211730.9390.9781000.175
2.864-3.0180.264570.21510760.21811330.9630.9741000.191
3.018-3.20.279530.19310160.19710690.9570.9781000.176
3.2-3.420.26510.2049610.20610120.9610.9761000.193
3.42-3.6930.274470.2169030.2199500.9630.9761000.209
3.693-4.0430.232440.1918390.1938830.970.9791000.189
4.043-4.5160.238410.1567620.1598030.9760.9861000.164
4.516-5.2070.239340.1596630.1626970.9730.9871000.174
5.207-6.3590.209320.1985910.1996230.9780.9811000.205
6.359-8.9160.201230.1444500.1464730.9760.9891000.162
8.916-48.3780.133160.1562900.1553070.9860.98299.67430.191

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