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- PDB-8h2d: The hypothetical protein from Mycobacterium tuberculosis mutant - E47A -

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Basic information

Entry
Database: PDB / ID: 8h2d
TitleThe hypothetical protein from Mycobacterium tuberculosis mutant - E47A
ComponentsUncharacterized protein Rv1546
KeywordsHYDROLASE / RNase
Function / homologyPolyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / plasma membrane / Alpha Beta / Uncharacterized protein Rv1546
Function and homology information
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKim, D.H. / Na, Y. / Lee, B.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Protein Sci. / Year: 2023
Title: Domain swapping of the C-terminal helix promotes the dimerization of a novel ribonuclease protein from Mycobacterium tuberculosis.
Authors: Kim, D.H. / Na, Y. / Chang, H. / Boo, J.H. / Kang, S.M. / Jin, C. / Kang, S.J. / Lee, S.Y. / Lee, B.J.
History
DepositionOct 5, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein Rv1546
B: Uncharacterized protein Rv1546


Theoretical massNumber of molelcules
Total (without water)30,9952
Polymers30,9952
Non-polymers00
Water32418
1
A: Uncharacterized protein Rv1546

A: Uncharacterized protein Rv1546


Theoretical massNumber of molelcules
Total (without water)30,9952
Polymers30,9952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3950 Å2
ΔGint-46 kcal/mol
Surface area13220 Å2
MethodPISA
2
B: Uncharacterized protein Rv1546

B: Uncharacterized protein Rv1546


Theoretical massNumber of molelcules
Total (without water)30,9952
Polymers30,9952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4010 Å2
ΔGint-47 kcal/mol
Surface area13760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.741, 99.050, 89.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Uncharacterized protein Rv1546


Mass: 15497.699 Da / Num. of mol.: 2 / Mutation: E47A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv1546, MTCY48.19c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WLU7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.17 Å3/Da / Density % sol: 43.39 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris, pH 8.5, 0.2 M ammonium sulfate and 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 6247 / % possible obs: 99.9 % / Redundancy: 12.81 % / Biso Wilson estimate: 87.06 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.79
Reflection shellResolution: 2.9→3.07 Å / Num. unique obs: 970 / CC1/2: 0.886

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PHENIX1.19_4092refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8H0H

8h0h


Resolution: 2.9→33.86 Å / SU ML: 0.2497 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.3853
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2612 306 4.9 %
Rwork0.219 5938 -
obs0.2211 6244 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.81 Å2
Refinement stepCycle: LAST / Resolution: 2.9→33.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2099 0 0 18 2117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00382141
X-RAY DIFFRACTIONf_angle_d0.70982892
X-RAY DIFFRACTIONf_chiral_restr0.0448320
X-RAY DIFFRACTIONf_plane_restr0.0075365
X-RAY DIFFRACTIONf_dihedral_angle_d4.8451294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.650.35661480.26782905X-RAY DIFFRACTION99.77
3.65-33.860.23451580.20523033X-RAY DIFFRACTION100

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