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- PDB-5ab6: Crystal structure of Trypanosoma brucei SCP2-thiolase like protei... -

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Basic information

Entry
Database: PDB / ID: 5ab6
TitleCrystal structure of Trypanosoma brucei SCP2-thiolase like protein (TbSLP) in complex with acetoacetyl-CoA.
ComponentsSCP2-THIOLASE LIKE PROTEIN
KeywordsTRANSPORT PROTEIN / COENZYME A / TRYPANOSOMA BRUCEI / SCP2-THIOLASE / SCP2-THIOLASE- LIKE PROTEIN / MALONYL-COA DECARBOXYLASE / GENE KNOCKOUT / LIPID METABOLISM
Function / homologyThiolase / acyltransferase activity, transferring groups other than amino-acyl groups / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta / ACETOACETYL-COENZYME A / Nonspecific lipid-transfer protein, putative
Function and homology information
Biological speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHarijan, R.K. / Kiema, T.R. / Wierenga, R.K.
CitationJournal: Proteins / Year: 2016
Title: The Scp2-Thiolase-Like Protein (Slp) of Trypanosoma Brucei is an Enzyme Involved in Lipid Metabolism.
Authors: Harijan, R.K. / Mazet, M. / Kiema, T.R. / Bouyssou, G. / Alexson, S.E.H. / Bergmann, U. / Moreau, P. / Michels, P.A.M. / Bringaud, F. / Wierenga, R.K.
History
DepositionAug 1, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SCP2-THIOLASE LIKE PROTEIN
B: SCP2-THIOLASE LIKE PROTEIN
C: SCP2-THIOLASE LIKE PROTEIN
D: SCP2-THIOLASE LIKE PROTEIN
E: SCP2-THIOLASE LIKE PROTEIN
F: SCP2-THIOLASE LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,36223
Polymers272,1956
Non-polymers6,16617
Water11,638646
1
E: SCP2-THIOLASE LIKE PROTEIN
F: SCP2-THIOLASE LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9159
Polymers90,7322
Non-polymers2,1847
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-60.1 kcal/mol
Surface area26410 Å2
MethodPISA
2
A: SCP2-THIOLASE LIKE PROTEIN
B: SCP2-THIOLASE LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7237
Polymers90,7322
Non-polymers1,9915
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-39.5 kcal/mol
Surface area26090 Å2
MethodPISA
3
C: SCP2-THIOLASE LIKE PROTEIN
D: SCP2-THIOLASE LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7237
Polymers90,7322
Non-polymers1,9915
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-39.9 kcal/mol
Surface area26220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.150, 65.972, 156.755
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A3 - 408
2010B3 - 408
1020A3 - 408
2020C3 - 408
1030A3 - 408
2030D3 - 408
1040A4 - 408
2040E4 - 408
1050A3 - 408
2050F3 - 408
1060B3 - 408
2060C3 - 408
1070B3 - 408
2070D3 - 408
1080B4 - 408
2080E4 - 408
1090B3 - 408
2090F3 - 408
10100C3 - 408
20100D3 - 408
10110C4 - 408
20110E4 - 408
10120C3 - 408
20120F3 - 408
10130D4 - 408
20130E4 - 408
10140D3 - 408
20140F3 - 408
10150E4 - 407
20150F4 - 407

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

NCS oper:
IDCodeMatrixVector
1given(-0.9956, -0.09326, -0.003459), (-0.09333, 0.9946, 0.04445), (-0.000705, 0.04458, -0.999)-57.14, -2.731, -0.2406
2given(-0.5511, -0.8344, 0.002536), (0.8339, -0.5509, -0.03306), (0.02898, -0.01611, 0.9995)-75.16, 40.84, -50.93
3given(0.4775, 0.8786, 0.005194), (0.8786, -0.4775, 0.007954), (0.009469, 0.000766, -1)13.9, 42.56, 52.72
4given(0.5528, -0.8333, 0.00145), (-0.833, -0.5526, 0.02606), (-0.02091, -0.01561, -0.9997)-41.3, -7.064, -52.67
5given(-0.4688, 0.8833, -0.001062), (-0.8833, -0.4688, -0.004607), (-0.004567, -0.001221, 1)-15.24, -7.419, 52.32
6given(0.4709, 0.8822, -0.000143), (0.8821, -0.4709, 0.01144), (0.01003, -0.005513, -0.9999)13.91, 42.76, 52.64
7given(-0.5573, -0.8303, -0.00512), (0.8298, -0.5568, -0.0371), (0.02795, -0.02493, 0.9993)-75, 40.78, -51.14
8given(-0.4726, 0.8812, -0.003184), (-0.8811, -0.4726, -0.01881), (-0.01808, -0.006083, 0.9998)-15.33, -8.126, 52.13
9given(0.5495, -0.8355, 0.000832), (-0.8349, -0.549, 0.03993), (-0.03291, -0.02264, -0.9992)-41.31, -6.238, -52.86
10given(0.4699, -0.8824, -0.02515), (-0.8826, -0.4702, 0.007446), (-0.01839, 0.0187, -0.9997)-44.64, -76.93, 103.8
11given(-1, -0.001978, -0.008037), (-0.001982, 1, 0.000533), (0.008036, 0.000549, -1)-58.66, -1.828, -0.06805
12given(-0.4781, -0.8779, 0.02563), (0.878, -0.4785, -0.01257), (0.02329, 0.01649, 0.9996)-70.28, -25.06, 104.9
13given(-0.4682, -0.8835, 0.01411), (0.8835, -0.4684, -0.01185), (0.01707, 0.006917, 0.9998)-70.96, -24.89, 104.7
14given(-0.9999, 0.009738, 0.00489), (0.009748, 1, 0.001958), (-0.004871, 0.002006, -1)-57.83, -1.744, -0.1461
15given(0.4765, 0.879, -0.01755), (0.879, -0.4767, -0.01203), (-0.01894, -0.009689, -0.9998)12.51, -23.15, -104.9

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Components

#1: Protein
SCP2-THIOLASE LIKE PROTEIN


Mass: 45365.898 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Strain: EATRO1125 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C9ZUV7
#2: Chemical
ChemComp-CAA / ACETOACETYL-COENZYME A / Acetoacetyl-CoA


Mass: 851.607 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C25H40N7O18P3S
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 646 / 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: 2.3 Å3/Da / Density % sol: 48.5 % / Description: NONE
Crystal growpH: 4.6
Details: 100 MM SODIUM ACETATE (PH 4.6), 2.0 M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2013 / Details: COMPOUND REFRACTIVE LENSES
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→29.41 Å / Num. obs: 184266 / % possible obs: 98.5 % / Observed criterion σ(I): 2.2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→29.43 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.536 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26422 9153 5 %RANDOM
Rwork0.24762 ---
obs0.24844 174242 97.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.445 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å20.05 Å2
2--0.39 Å20 Å2
3----1.24 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17592 0 379 646 18617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01918384
X-RAY DIFFRACTIONr_bond_other_d0.0030.0217552
X-RAY DIFFRACTIONr_angle_refined_deg1.1011.98925006
X-RAY DIFFRACTIONr_angle_other_deg0.884340355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.16652366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.99523.484706
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.808152847
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.48215115
X-RAY DIFFRACTIONr_chiral_restr0.0610.22827
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02120803
X-RAY DIFFRACTIONr_gen_planes_other0.0030.024054
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A244420.05
12B244420.05
21A243290.06
22C243290.06
31A243620.06
32D243620.06
41A244070.05
42E244070.05
51A244940.05
52F244940.05
61B242280.06
62C242280.06
71B243480.06
72D243480.06
81B243630.05
82E243630.05
91B244630.06
92F244630.06
101C240470.07
102D240470.07
111C242100.06
112E242100.06
121C242240.06
122F242240.06
131D242250.06
132E242250.06
141D244730.06
142F244730.06
151E243880.05
152F243880.05
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 641 -
Rwork0.428 12721 -
obs--97.09 %

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