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- PDB-4bi9: Crystal structure of wild-type SCP2 thiolase from Trypanosoma brucei. -

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Basic information

Entry
Database: PDB / ID: 4bi9
TitleCrystal structure of wild-type SCP2 thiolase from Trypanosoma brucei.
Components3-KETOACYL-COA THIOLASE, PUTATIVE
KeywordsTRANSFERASE
Function / homology
Function and homology information


propanoyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / kinetoplast / acyltransferase activity / lipid transport / lipid binding / mitochondrion
Similarity search - Function
: / Thiolase C-terminal domain-like / Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like ...: / Thiolase C-terminal domain-like / Thiolase, conserved site / Thiolases signature 2. / 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
propanoyl-CoA C-acyltransferase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsHarijan, R.K. / Kiema, T.-R. / Weiss, M.S. / Michels, P.A.M. / Wierenga, R.K.
CitationJournal: Biochem.J. / Year: 2013
Title: Crystal Structures of Scp2-Thiolases of Trypanosomatidae, Human Pathogens Causing Widespread Tropical Diseases: The Importance for Catalysis of the Cysteine of the Unique Hdcf Loop.
Authors: Harijan, R.K. / Kiema, T.-R. / Karjalainen, M.P. / Janardan, N. / Murthy, M.R.N. / Weiss, M.S. / Michels, P.A.M. / Wierenga, R.K.
History
DepositionApr 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-KETOACYL-COA THIOLASE, PUTATIVE
B: 3-KETOACYL-COA THIOLASE, PUTATIVE
C: 3-KETOACYL-COA THIOLASE, PUTATIVE
D: 3-KETOACYL-COA THIOLASE, PUTATIVE


Theoretical massNumber of molelcules
Total (without water)192,4224
Polymers192,4224
Non-polymers00
Water97354
1
A: 3-KETOACYL-COA THIOLASE, PUTATIVE
B: 3-KETOACYL-COA THIOLASE, PUTATIVE


Theoretical massNumber of molelcules
Total (without water)96,2112
Polymers96,2112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-12.1 kcal/mol
Surface area27680 Å2
MethodPISA
2
C: 3-KETOACYL-COA THIOLASE, PUTATIVE
D: 3-KETOACYL-COA THIOLASE, PUTATIVE


Theoretical massNumber of molelcules
Total (without water)96,2112
Polymers96,2112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-11.9 kcal/mol
Surface area27780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.139, 59.139, 377.575
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 12:33 OR RESSEQ 43:65 OR RESSEQ...
211CHAIN B AND (RESSEQ 12:33 OR RESSEQ 43:65 OR RESSEQ...
311CHAIN C AND (RESSEQ 12:33 OR RESSEQ 43:65 OR RESSEQ...
411CHAIN D AND (RESSEQ 12:33 OR RESSEQ 43:65 OR RESSEQ...

NCS oper:
IDCodeMatrixVector
1given(-0.5128, 0.8582, -0.02452), (0.8581, 0.5114, -0.04587), (-0.02682, -0.04456, -0.9986)9.02684, -1.69679, 115.063
2given(0.4313, -0.9022, -0.007907), (0.9021, 0.431, 0.02203), (-0.01647, -0.01663, 0.9997)126.324, 4.53252, 65.74
3given(0.4128, 0.9101, -0.03557), (0.9082, -0.4143, -0.0601), (-0.06943, -0.007497, -0.9976)-52.2636, 87.1102, 50.9652
4given(0.553, 0.8332, -0.004678), (0.8324, -0.5527, -0.04015), (-0.03604, 0.01831, -0.9992)-53.4833, 105.998, 46.2001
5given(0.5695, -0.822, -0.006226), (0.8218, 0.5695, -0.01709), (0.01759, 0.004614, 0.9998)109.358, -4.32948, 61.403
6given(0.9984, 0.01933, -0.05371), (0.02056, -0.9995, 0.02255), (-0.05325, -0.02362, -0.9983)-2.3329, 196.932, -11.523

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Components

#1: Protein
3-KETOACYL-COA THIOLASE, PUTATIVE / SCP2 THIOLASE


Mass: 48105.523 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Strain: 927/4 GUTAT10.1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q57XD5, acetyl-CoA C-acyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.1 Å3/Da / Density % sol: 40.4 % / Description: NONE
Crystal growpH: 5.6
Details: 100MM SODIUM CITRATE PH5.6, 200MM AMMONIUM ACETATE AND 30% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 5, 2011 / Details: MIRRORS
RadiationMonochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.5
ReflectionResolution: 2.45→50.75 Å / Num. obs: 49740 / % possible obs: 91.5 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.5
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2 / % possible all: 90.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZBG

3zbg


Resolution: 2.45→50.751 Å / σ(F): 1.97 / Phase error: 29.96 / Stereochemistry target values: TWIN_LSQ_F
Details: THE RESIDUES FROM 1-11, 34-43 AND 102- 104 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2422 2694 5.4 %
Rwork0.2241 --
obs0.2257 49662 91.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→50.751 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12295 0 0 54 12349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912479
X-RAY DIFFRACTIONf_angle_d1.26916872
X-RAY DIFFRACTIONf_dihedral_angle_d15.9354480
X-RAY DIFFRACTIONf_chiral_restr0.1041945
X-RAY DIFFRACTIONf_plane_restr0.0042216
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3045X-RAY DIFFRACTIONPOSITIONAL
12B3045X-RAY DIFFRACTIONPOSITIONAL0.053
13C3045X-RAY DIFFRACTIONPOSITIONAL0.041
14D3045X-RAY DIFFRACTIONPOSITIONAL0.05
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4508-2.49790.36461350.35872591X-RAY DIFFRACTION87
2.4979-2.54890.34171340.34822565X-RAY DIFFRACTION86
2.5489-2.60430.36941550.32452567X-RAY DIFFRACTION85
2.6043-2.66480.2991320.33062598X-RAY DIFFRACTION86
2.6648-2.73140.31251300.32332529X-RAY DIFFRACTION85
2.7314-2.80520.35111210.31882619X-RAY DIFFRACTION85
2.8052-2.88770.2831560.30062413X-RAY DIFFRACTION82
2.8877-2.98090.31251250.30282549X-RAY DIFFRACTION84
2.9809-3.08740.29641470.28832471X-RAY DIFFRACTION82
3.0874-3.21090.27661300.27742459X-RAY DIFFRACTION82
3.2109-3.35690.27621400.24532490X-RAY DIFFRACTION83
3.3569-3.53360.26921460.23192553X-RAY DIFFRACTION84
3.5336-3.75470.22011210.2142633X-RAY DIFFRACTION87
3.7547-4.04410.21491190.1972717X-RAY DIFFRACTION90
4.0441-4.45020.1831590.17752804X-RAY DIFFRACTION92
4.4502-5.0920.23551440.19092811X-RAY DIFFRACTION94
5.092-6.40730.22391470.21172882X-RAY DIFFRACTION95
6.4073-32.45730.19461520.16172855X-RAY DIFFRACTION95

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