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- PDB-4zrc: Crystal structure of MSM-13, a putative T1-like thiolase from Myc... -

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Basic information

Entry
Database: PDB / ID: 4zrc
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 / Resolution: 2.7 Å
AuthorsJanardan, N. / Harijan, R.K. / Keima, T.R. / Wierenga, R. / Murthy, M.R.N.
Funding support India, 1items
OrganizationGrant numberCountry
Department of BiotechnologyBT/IN/FINNISH/27/MRNM/2009 India
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
DepositionMay 12, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: 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 / diffrn_radiation_wavelength / 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


Theoretical massNumber of molelcules
Total (without water)175,3474
Polymers175,3474
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13810 Å2
ΔGint-41.2 kcal/mol
Surface area52860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.460, 104.140, 104.570
Angle α, β, γ (deg.)90.00, 107.53, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1METMETGLNGLNAA3 - 4059 - 411
2METMETGLUGLUBB3 - 4069 - 412
3ARGARGGLUGLUCC4 - 40610 - 412
4ARGARGGLNGLNDD4 - 40510 - 411

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.760978, -0.134008, 0.634787), (-0.113757, -0.935716, -0.333907), (0.638727, -0.326308, 0.696815)37.86846, -7.1959, -15.67977
3given(0.75739, 0.041412, -0.651649), (0.013169, -0.998753, -0.048165), (-0.65283, 0.027898, -0.75699)18.43372, -16.53354, 49.55629
4given(-0.994192, 0.105347, 0.021989), (0.106131, 0.925925, 0.36249), (0.017827, 0.362719, -0.931728)57.38278, -9.40311, 36.44238

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Components

#1: Protein
Beta-ketothiolase


Mass: 43836.699 Da / Num. of mol.: 4
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.: 103 / 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: 2.23 Å3/Da / Density % sol: 44.95 %
Crystal growTemperature: 295 K / Method: microbatch
Details: 0.2M sodium acetate trihydrate, 0.1M sodium cacodylatetrihydrate pH 6.5, 30% PEG 8000, 5% n-octyl-D-glucoside

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.43→47.52 Å / Num. all: 201832 / Num. obs: 201832 / % possible obs: 98.92 % / Redundancy: 1 % / Net I/σ(I): 8.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.7→47.52 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.843 / SU B: 16.328 / SU ML: 0.324 / Cross valid method: THROUGHOUT / ESU R Free: 0.42
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.28329 2129 5.1 %RANDOM
Rwork0.22295 ---
obs0.2259 39995 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.306 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20.01 Å2
2---0.05 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.7→47.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11483 0 0 103 11586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01911644
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.96815783
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49551560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.72923.354477
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.746151832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.05215112
X-RAY DIFFRACTIONr_chiral_restr0.1030.21822
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218857
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_it2.8814.466297
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.586.6747838
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9344.5865347
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.93936.28916793
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: 2686 / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Auth asym-IDRms dev position (Å)
A5.03
B5.68
C5.63
D5.54
LS refinement shellResolution: 2.698→2.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 141 -
Rwork0.295 2578 -
obs--87.57 %

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