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- PDB-5lot: Crystal structure of SCP2 thiolase from Leishmania mexicana. Comp... -

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Basic information

Entry
Database: PDB / ID: 5lot
TitleCrystal structure of SCP2 thiolase from Leishmania mexicana. Complex of the C123A mutant with acetyl-CoA.
Components3-ketoacyl-CoA thiolase-like protein
KeywordsTRANSFERASE / Leishmania mexicana / SCP2-thiolase / acetoacetyl-coA / lipid metabolism
Function / homology
Function and homology information


propanoyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / lipid transport / lipid binding
Similarity search - Function
: / Thiolase C-terminal domain-like / Thiolase, conserved site / Thiolases signature 2. / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 ...: / Thiolase C-terminal domain-like / Thiolase, conserved site / Thiolases signature 2. / 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
ACETYL COENZYME *A / propanoyl-CoA C-acyltransferase
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsHarijan, R.K. / Kiema, T.-R. / Wierenga, R.K.
Funding support Finland, 3items
OrganizationGrant numberCountry
Academy of Finland131795 Finland
BioStruct-X283570 Finland
European Commissions Seventh FrameworkFP7/2007-2013 Finland
CitationJournal: Protein Eng. Des. Sel. / Year: 2017
Title: Crystallographic substrate binding studies of Leishmania mexicana SCP2-thiolase (type-2): unique features of oxyanion hole-1.
Authors: Harijan, R.K. / Kiema, T.R. / Syed, S.M. / Qadir, I. / Mazet, M. / Bringaud, F. / Michels, P.A.M. / Wierenga, R.K.
History
DepositionAug 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 3-ketoacyl-CoA thiolase-like protein
B: 3-ketoacyl-CoA thiolase-like protein
C: 3-ketoacyl-CoA thiolase-like protein
D: 3-ketoacyl-CoA thiolase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,3327
Polymers196,9044
Non-polymers2,4293
Water11,422634
1
A: 3-ketoacyl-CoA thiolase-like protein
B: 3-ketoacyl-CoA thiolase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0714
Polymers98,4522
Non-polymers1,6192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-29 kcal/mol
Surface area28110 Å2
MethodPISA
2
C: 3-ketoacyl-CoA thiolase-like protein
D: 3-ketoacyl-CoA thiolase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2613
Polymers98,4522
Non-polymers8101
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-26 kcal/mol
Surface area28350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.701, 89.889, 126.332
Angle α, β, γ (deg.)90.000, 105.780, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 12 - 441 / Label seq-ID: 28 - 457

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
3-ketoacyl-CoA thiolase-like protein


Mass: 49225.926 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (strain MHOM/GT/2001/U1103) (eukaryote)
Strain: MHOM/GT/2001/U1103 / Gene: LMXM_23_0690 / Production host: Escherichia coli (E. coli) / References: UniProt: E9AW84, acetyl-CoA C-acyltransferase
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 634 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris, pH 8.0, 0.2 M lithium chloride and 20% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Sep 21, 2014
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→47.3 Å / Num. obs: 76184 / % possible obs: 98.2 % / Redundancy: 7.1 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.6
Reflection shellResolution: 2.25→2.35 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.4 / % possible all: 89

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
PDB_EXTRACT3.2data extraction
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZBN

3zbn


Resolution: 2.25→47.3 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.89 / SU B: 8.075 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.392 / ESU R Free: 0.249
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2552 3952 4.9 %RANDOM
Rwork0.2135 ---
obs0.2155 76184 98.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 131.64 Å2 / Biso mean: 30.358 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å2-0.08 Å2
2---0.56 Å20 Å2
3----0.86 Å2
Refinement stepCycle: final / Resolution: 2.25→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12892 0 153 634 13679
Biso mean--63.47 26.35 -
Num. residues----1720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01913263
X-RAY DIFFRACTIONr_bond_other_d0.0070.0212680
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.97617905
X-RAY DIFFRACTIONr_angle_other_deg1.166329202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1951716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.12424.748556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.38152268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4511568
X-RAY DIFFRACTIONr_chiral_restr0.0830.21986
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215229
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022938
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A265050.07
12B265050.07
21A269360.05
22C269360.05
31A265710.06
32D265710.06
41B264910.07
42C264910.07
51B270760.05
52D270760.05
61C264050.07
62D264050.07
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 232 -
Rwork0.335 4955 -
all-5187 -
obs--86.18 %

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