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- PDB-5cbq: Crystal structure of a T1-like thiolase from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 5cbq
TitleCrystal structure of a T1-like thiolase from Mycobacterium smegmatis
ComponentsBeta-ketothiolase
KeywordsTRANSFERASE / Thiolase / Mycobacterium smegmatis / coenzyme A
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 / Resolution: 2.45 Å
AuthorsJanardan, N. / 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
DepositionJul 1, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)263,0206
Polymers263,0206
Non-polymers00
Water6,053336
1
A: Beta-ketothiolase
B: Beta-ketothiolase
C: Beta-ketothiolase
D: Beta-ketothiolase


Theoretical massNumber of molelcules
Total (without water)175,3474
Polymers175,3474
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14040 Å2
ΔGint-48.4 kcal/mol
Surface area50730 Å2
MethodPISA
2
E: Beta-ketothiolase
F: Beta-ketothiolase

E: Beta-ketothiolase
F: Beta-ketothiolase


Theoretical massNumber of molelcules
Total (without water)175,3474
Polymers175,3474
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area13610 Å2
ΔGint-48.7 kcal/mol
Surface area51320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.460, 181.470, 271.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / Refine code: 1

Dom-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1VALVALAA4 - 40410 - 410
2GLNGLNBB4 - 40510 - 411
3GLNGLNCC4 - 40510 - 411
4GLUGLUDD4 - 40610 - 412
5GLNGLNEE4 - 40510 - 411
6VALVALFF4 - 40410 - 410

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.356105, 0.911604, 0.205347), (0.915268, 0.295976, 0.273283), (0.188348, 0.285265, -0.93976)-10.0818, -35.44979, 198.04489
3given(0.364495, -0.921258, -0.135745), (-0.924349, -0.375604, 0.067091), (-0.112795, 0.101022, -0.988469)74.97512, 81.51023, 223.23468
4given(-0.995769, 0.014715, -0.090702), (0.021182, -0.923752, -0.382405), (-0.089413, -0.382709, 0.919532)82.54122, 119.4108, 26.37203
5given(-0.528788, 0.844561, -0.084264), (-0.76711, -0.518047, -0.378377), (-0.363215, -0.135441, 0.921808)-27.30582, 108.50759, 59.6585
6given(-0.58423, -0.799619, -0.138867), (-0.811307, 0.579914, 0.074027), (0.021337, 0.155912, -0.98754)111.63689, -12.77686, 166.1734

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Components

#1: Protein
Beta-ketothiolase


Mass: 43836.699 Da / Num. of mol.: 6
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.: 336 / Source method: isolated from a natural source / Formula: H2O
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: 2.76 Å3/Da / Density % sol: 55.43 %
Crystal growTemperature: 293 K / Method: microbatch / Details: 20% PEG 3350, 0.15 M calcium chloride dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.45→135.9 Å / Num. obs: 91315 / % possible obs: 89.09 % / Redundancy: 1.8 % / Net I/σ(I): 7.5
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.7 / % possible all: 84.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.45→135.87 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.893 / SU B: 10.677 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 0.641 / ESU R Free: 0.316
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.26757 4603 5 %RANDOM
Rwork0.22575 ---
obs0.22782 86712 89.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.142 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.01 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.45→135.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17367 0 0 336 17703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01917843
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.831.96924227
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.38752393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46523.393728
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.246152853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.40415168
X-RAY DIFFRACTIONr_chiral_restr0.1060.22816
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113558
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9573.8279587
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.5475.73111972
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7364.0948252
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.97331.72626519
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2799 / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Auth asym-IDRms dev position (Å)
A7.66
B7.74
C6.59
D8.55
E6.18
F10.25
LS refinement shellResolution: 2.453→2.517 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 314 -
Rwork0.312 5998 -
obs--83.95 %

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