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- PDB-8h0h: Hypotethical protein from Mycobacterium tuberculsosis -

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Basic information

Entry
Database: PDB / ID: 8h0h
TitleHypotethical protein from Mycobacterium tuberculsosis
ComponentsUncharacterized protein Rv1546
KeywordsHYDROLASE
Function / homologyPolyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / START-like domain superfamily / plasma membrane / Uncharacterized protein Rv1546
Function and homology information
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.74 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
DepositionSep 29, 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
C: Uncharacterized protein Rv1546
A: Uncharacterized protein Rv1546
D: Uncharacterized protein Rv1546
B: Uncharacterized protein Rv1546


Theoretical massNumber of molelcules
Total (without water)62,7994
Polymers62,7994
Non-polymers00
Water99155
1
C: Uncharacterized protein Rv1546
D: Uncharacterized protein Rv1546


Theoretical massNumber of molelcules
Total (without water)31,4002
Polymers31,4002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-42 kcal/mol
Surface area14170 Å2
MethodPISA
2
A: Uncharacterized protein Rv1546
B: Uncharacterized protein Rv1546


Theoretical massNumber of molelcules
Total (without water)31,4002
Polymers31,4002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-40 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.197, 87.518, 55.907
Angle α, β, γ (deg.)90.000, 94.510, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Uncharacterized protein Rv1546


Mass: 15699.864 Da / Num. of mol.: 4
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.: 55 / 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: 2.14 Å3/Da / Density % sol: 42.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis/Tris Propane/HCl, pH 6.5, 0.2 M sodium fluoride and 20% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.74→50 Å / Num. obs: 13538 / % possible obs: 96.4 % / Redundancy: 4.5 % / Biso Wilson estimate: 39.57 Å2 / CC1/2: 0.96 / Net I/σ(I): 8.1
Reflection shellResolution: 2.75→2.8 Å / Num. unique obs: 636 / CC1/2: 0.87

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.74→47.01 Å / SU ML: 0.3755 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.5465
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2541 674 4.99 %
Rwork0.1997 12840 -
obs0.2024 13514 95.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.72 Å2
Refinement stepCycle: LAST / Resolution: 2.74→47.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4392 0 0 55 4447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00264488
X-RAY DIFFRACTIONf_angle_d0.5356076
X-RAY DIFFRACTIONf_chiral_restr0.0412664
X-RAY DIFFRACTIONf_plane_restr0.005780
X-RAY DIFFRACTIONf_dihedral_angle_d4.2018620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.74-2.950.31821140.26582368X-RAY DIFFRACTION88.64
2.95-3.240.29491560.23922590X-RAY DIFFRACTION97.07
3.24-3.710.27161260.2122607X-RAY DIFFRACTION97.4
3.71-4.680.22341150.16982631X-RAY DIFFRACTION97.76
4.68-47.010.22791630.18022644X-RAY DIFFRACTION97.98

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