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- PDB-5byv: Crystal structure of MSM-13, a putative T1-like thiolase from Myc... -

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Basic information

Entry
Database: PDB / ID: 5byv
TitleCrystal structure of MSM-13, a putative T1-like thiolase from Mycobacterium smegmatis
ComponentsBeta-ketothiolase
KeywordsTRANSFERASE / thiolase / mycobacterium smegmatis / T1-like / tetrameric
Function / homology
Function and homology information


acetyl-CoA C-acetyltransferase / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.162 Å
AuthorsJanardan, N. / Harijan, R.K. / Keima, T.R. / Wierenga, R. / Murthy, M.R.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural characterization of a mitochondrial 3-ketoacyl-CoA (T1)-like thiolase from Mycobacterium smegmatis
Authors: Janardan, N. / Harijan, R.K. / Kiema, T.R. / Wierenga, R.K. / Murthy, M.R.
History
DepositionJun 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-ketothiolase
B: Beta-ketothiolase
C: Beta-ketothiolase
D: Beta-ketothiolase
E: Beta-ketothiolase
F: Beta-ketothiolase
G: Beta-ketothiolase
H: Beta-ketothiolase
J: Beta-ketothiolase
K: Beta-ketothiolase
L: Beta-ketothiolase
M: Beta-ketothiolase


Theoretical massNumber of molelcules
Total (without water)516,09412
Polymers516,09412
Non-polymers00
Water27,4911526
1
A: Beta-ketothiolase
B: Beta-ketothiolase
C: Beta-ketothiolase
D: Beta-ketothiolase


Theoretical massNumber of molelcules
Total (without water)172,0314
Polymers172,0314
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13800 Å2
ΔGint-47 kcal/mol
Surface area50880 Å2
MethodPISA
2
E: Beta-ketothiolase
F: Beta-ketothiolase
G: Beta-ketothiolase
H: Beta-ketothiolase


Theoretical massNumber of molelcules
Total (without water)172,0314
Polymers172,0314
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13820 Å2
ΔGint-51 kcal/mol
Surface area51520 Å2
MethodPISA
3
J: Beta-ketothiolase
K: Beta-ketothiolase
L: Beta-ketothiolase
M: Beta-ketothiolase


Theoretical massNumber of molelcules
Total (without water)172,0314
Polymers172,0314
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13790 Å2
ΔGint-47 kcal/mol
Surface area51550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.959, 190.959, 264.681
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Beta-ketothiolase


Mass: 43007.824 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria)
Strain: MC2 155 / Gene: MSMEG_2207 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QUH3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1526 / 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: 2.7 Å3/Da / Density % sol: 54.43 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6
Details: 45% PEG 200, 0.1M MES monohydrate pH 6.0, 0.07M calcium chloride dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.16→45.193 Å / Num. obs: 290242 / % possible obs: 99.94 % / Redundancy: 1.9 % / Net I/σ(I): 12.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZEC

4zec


Resolution: 2.162→45.193 Å / Cross valid method: FREE R-VALUE / σ(F): 0.2 / Phase error: 24.35 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2 14685 5.06 %
Rwork0.1691 --
obs0.1707 290242 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.162→45.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35174 0 0 1526 36700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00935691
X-RAY DIFFRACTIONf_angle_d1.22248405
X-RAY DIFFRACTIONf_dihedral_angle_d15.61413127
X-RAY DIFFRACTIONf_chiral_restr0.0445619
X-RAY DIFFRACTIONf_plane_restr0.0066437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1623-2.19950.25397010.227413723X-RAY DIFFRACTION95
2.1995-2.23950.24817710.220913741X-RAY DIFFRACTION95
2.2395-2.28260.23587560.21113759X-RAY DIFFRACTION95
2.2826-2.32920.24547910.205113750X-RAY DIFFRACTION95
2.3292-2.37980.23167890.204913654X-RAY DIFFRACTION94
2.3798-2.43520.22147230.20113779X-RAY DIFFRACTION95
2.4352-2.49610.23027430.202313709X-RAY DIFFRACTION95
2.4961-2.56360.22077330.194913762X-RAY DIFFRACTION95
2.5636-2.6390.22446880.187713817X-RAY DIFFRACTION95
2.639-2.72420.21997320.1913766X-RAY DIFFRACTION95
2.7242-2.82150.22916950.185913806X-RAY DIFFRACTION95
2.8215-2.93450.22077340.181713770X-RAY DIFFRACTION95
2.9345-3.0680.19687490.177113761X-RAY DIFFRACTION95
3.068-3.22970.19476850.171713858X-RAY DIFFRACTION95
3.2297-3.4320.20177560.167313747X-RAY DIFFRACTION95
3.432-3.69690.18117450.151313749X-RAY DIFFRACTION95
3.6969-4.06870.17116810.140313869X-RAY DIFFRACTION95
4.0687-4.65690.1617900.126713766X-RAY DIFFRACTION94
4.6569-5.86520.19577010.153613815X-RAY DIFFRACTION95
5.8652-45.20320.17957170.157913871X-RAY DIFFRACTION95

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