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- PDB-4bia: Crystal structure of SCP2 thiolase from Trypanosoma brucei: The C... -

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Basic information

Entry
Database: PDB / ID: 4bia
TitleCrystal structure of SCP2 thiolase from Trypanosoma brucei: The C337A mutant.
Components3-KETOACYL-COA THIOLASE, PUTATIVE
KeywordsTRANSFERASE
Function / homology
Function and homology information


propanoyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / kinetoplast / acyltransferase activity / mitochondrion
Similarity search - Function
Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like ...Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / 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 / MOLECULAR REPLACEMENT / Resolution: 2.9 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 1.2Feb 4, 2015Group: Data collection
Revision 1.3Dec 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

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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)192,2944
Polymers192,2944
Non-polymers00
Water50428
1
C: 3-KETOACYL-COA THIOLASE, PUTATIVE
D: 3-KETOACYL-COA THIOLASE, PUTATIVE


Theoretical massNumber of molelcules
Total (without water)96,1472
Polymers96,1472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-13.5 kcal/mol
Surface area28410 Å2
MethodPISA
2
A: 3-KETOACYL-COA THIOLASE, PUTATIVE
B: 3-KETOACYL-COA THIOLASE, PUTATIVE


Theoretical massNumber of molelcules
Total (without water)96,1472
Polymers96,1472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-13.9 kcal/mol
Surface area28240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.128, 60.128, 375.495
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: 101 OR RESSEQ 105:438 )
211CHAIN B AND (RESSEQ 12:33 OR RESSEQ 43: 101 OR RESSEQ 105:438 )
311CHAIN C AND (RESSEQ 12:33 OR RESSEQ 43: 101 OR RESSEQ 105:438 )
411CHAIN D AND (RESSEQ 12:33 OR RESSEQ 43: 101 OR RESSEQ 105:438 )

NCS oper:
IDCodeMatrixVector
1given(-0.4988, -0.8667, -0.001431), (-0.8667, 0.4988, 0.000599), (0.000195, 0.001539, -1)29.849, 17.1289, 110.655
2given(0.4857, -0.8734, 0.03602), (0.8735, 0.4866, 0.01868), (-0.03384, 0.02239, 0.9992)-28.6472, -89.8361, 66.1892
3given(-0.9992, -0.01514, -0.03611), (-0.01447, 0.9997, -0.01871), (0.03638, -0.01817, -0.9992)119.586, -1.16653, 44.5609
4given(-0.9994, 0.01349, -0.03288), (0.01416, 0.9997, -0.02035), (0.0326, -0.0208, -0.9993)121.847, -2.68474, 44.5675
5given(0.5113, -0.8587, 0.03368), (0.8587, 0.5121, 0.02039), (-0.03476, 0.0185, 0.9992)-28.9241, -86.9747, 65.9272
6given(-0.5, 0.866, -0.000794), (0.866, 0.5, 5.8E-5), (0.000447, -0.000658, -1)150.179, -86.742, -14.6705

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Components

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


Mass: 48073.461 Da / Num. of mol.: 4 / Mutation: YES
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.: 28 / 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: 41.9 % / Description: NONE
Crystal growpH: 5.5
Details: 100MM BIS TRIS PH5.5, 200MM LITHIUM SULFATE AND 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Oct 2, 2012 / Details: HELIOS MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.5
ReflectionResolution: 2.9→41.72 Å / Num. obs: 33721 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 9.9
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

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

3zbg


Resolution: 2.9→37.363 Å / σ(F): 1.96 / Phase error: 32.73 / Stereochemistry target values: TWIN_LSQ_F
Details: THE RESIDUES FROM 1-11, 34-43 AND 102- 104 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2956 1701 5.1 %
Rwork0.267 --
obs0.2683 33524 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→37.363 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12291 0 0 28 12319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512476
X-RAY DIFFRACTIONf_angle_d1.09116871
X-RAY DIFFRACTIONf_dihedral_angle_d14.5644477
X-RAY DIFFRACTIONf_chiral_restr0.0921945
X-RAY DIFFRACTIONf_plane_restr0.0042217
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3054X-RAY DIFFRACTIONPOSITIONAL
12B3054X-RAY DIFFRACTIONPOSITIONAL0.042
13C3054X-RAY DIFFRACTIONPOSITIONAL0.045
14D3054X-RAY DIFFRACTIONPOSITIONAL0.046
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9007-2.98590.34381590.31762676X-RAY DIFFRACTION94
2.9859-3.08210.35751550.32112578X-RAY DIFFRACTION94
3.0821-3.19210.31111420.33722702X-RAY DIFFRACTION95
3.1921-3.31960.3341500.32072652X-RAY DIFFRACTION94
3.3196-3.47030.34791390.30982627X-RAY DIFFRACTION94
3.4703-3.65270.3031390.29972566X-RAY DIFFRACTION94
3.6527-3.88070.32991180.27052721X-RAY DIFFRACTION95
3.8807-4.17890.29671480.25672627X-RAY DIFFRACTION94
4.1789-4.59690.26221470.23062646X-RAY DIFFRACTION94
4.5969-5.25630.30841400.25312627X-RAY DIFFRACTION95
5.2563-6.60060.26211370.26152682X-RAY DIFFRACTION95
6.6006-24.39210.25311250.22642660X-RAY DIFFRACTION95

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