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- PDB-9fb1: Crystal structure of Rv2242 regulator N-terminal fragment (1-160) -

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Basic information

Entry
Database: PDB / ID: 9fb1
TitleCrystal structure of Rv2242 regulator N-terminal fragment (1-160)
ComponentsUncharacterized protein Rv2242
KeywordsTRANSCRIPTION / NONHEME GLOBIN SENSOR DOMAIN / 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 / MOLECULAR REPLACEMENT / Resolution: 3.59 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 11, 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

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Assembly

Deposited unit
A: Uncharacterized protein Rv2242
B: Uncharacterized protein Rv2242
C: Uncharacterized protein Rv2242
D: Uncharacterized protein Rv2242


Theoretical massNumber of molelcules
Total (without water)80,6794
Polymers80,6794
Non-polymers00
Water00
1
A: Uncharacterized protein Rv2242

A: Uncharacterized protein Rv2242


  • defined by author&software
  • Evidence: gel filtration, Remark 350 in orthogonal coordinates REMARK 350 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA v1.52 [20/10/2014] REMARK 350 ...Evidence: gel filtration, Remark 350 in orthogonal coordinates REMARK 350 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA v1.52 [20/10/2014] REMARK 350 TOTAL BURIED SURFACE AREA: 2290 ANGSTROM**2 REMARK 350 SURFACE AREA FOR THE COMPLEX: 14660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 IN ADDITION APPLY THE FOLLOWING TO CHAINS: D REMARK 350 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 107.19000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 44.12825
  • 40.3 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)40,3402
Polymers40,3402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,-y+1,-z+1/21
Buried area2470 Å2
ΔGint-16 kcal/mol
Surface area15780 Å2
MethodPISA
2
B: Uncharacterized protein Rv2242

B: Uncharacterized protein Rv2242


  • defined by author&software
  • Evidence: gel filtration, Remark 350 in orthogonal coordinates REMARK 350 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA v1.52 [20/10/2014] REMARK 350 ...Evidence: gel filtration, Remark 350 in orthogonal coordinates REMARK 350 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA v1.52 [20/10/2014] REMARK 350 TOTAL BURIED SURFACE AREA: 2150 ANGSTROM**2 REMARK 350 SURFACE AREA FOR THE COMPLEX: 16270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 107.19000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 88.25650
  • 40.3 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)40,3402
Polymers40,3402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area2150 Å2
ΔGint-19 kcal/mol
Surface area15260 Å2
MethodPISA
3
D: Uncharacterized protein Rv2242

C: Uncharacterized protein Rv2242


  • defined by author&software
  • Evidence: gel filtration, Remark 350 in orthogonal coordinates REMARK 350 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA v1.52 [20/10/2014] REMARK 350 ...Evidence: gel filtration, Remark 350 in orthogonal coordinates REMARK 350 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA v1.52 [20/10/2014] REMARK 350 TOTAL BURIED SURFACE AREA: 1880 ANGSTROM**2 REMARK 350 SURFACE AREA FOR THE COMPLEX: 15390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000
  • 40.3 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)40,3402
Polymers40,3402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_565-y,-x+1,-z+1/41
Buried area2340 Å2
ΔGint-22 kcal/mol
Surface area14510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.190, 107.190, 176.513
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein
Uncharacterized protein Rv2242


Mass: 20169.836 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: Rv2242, MTCY427.23 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WPH5
Has protein modificationN

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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: 3.15 Å3/Da / Density % sol: 60.93 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 200 mM NaBr, 100 mM Bis-Tris propane, pH 8.5, 20% (w/w) PEG3350, temperature 293.15 K, vapor diffusion, hanging drop

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 3.59→57.57 Å / Num. obs: 10989 / % possible obs: 95 % / Redundancy: 26.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.169 / Rrim(I) all: 0.172 / Net I/σ(I): 11.3
Reflection shellResolution: 3.593→3.762 Å / Rmerge(I) obs: 1.628 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 549 / CC1/2: 0.822 / Rrim(I) all: 1.66 / % possible all: 76.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROC1.0.5data reduction
XDSVERSION Jun 30, 2023 BUILT=20230630data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.59→57.57 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.885 / SU B: 40.14 / SU ML: 0.61 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.822 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3249 535 4.9 %RANDOM
Rwork0.25 ---
obs0.2535 10454 87.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 423.38 Å2 / Biso mean: 161.346 Å2 / Biso min: 40.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å2-0 Å2-0 Å2
2--0.51 Å2-0 Å2
3----1.02 Å2
Refinement stepCycle: final / Resolution: 3.59→57.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4575 0 0 0 4575
Num. residues----584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0124653
X-RAY DIFFRACTIONr_angle_refined_deg1.8321.8386336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3185580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.809544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.20910771
X-RAY DIFFRACTIONr_chiral_restr0.1250.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023480
X-RAY DIFFRACTIONr_mcbond_it19.40915.7832332
X-RAY DIFFRACTIONr_mcangle_it30.34328.3052908
X-RAY DIFFRACTIONr_scbond_it22.16116.4112321
LS refinement shellResolution: 3.593→3.686 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 20 -
Rwork0.247 251 -
all-271 -
obs--29.91 %

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