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- PDB-3zbn: Crystal structure of SCP2 thiolase from Leishmania mexicana. Comp... -

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Basic information

Entry
Database: PDB / ID: 3zbn
TitleCrystal structure of SCP2 thiolase from Leishmania mexicana. Complex of the C123A mutant with Coenzyme A.
Components3-KETOACYL-COA THIOLASE-LIKE PROTEIN
KeywordsTRANSFERASE / COENZYME A TRANSFERASE
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
COENZYME A / propanoyl-CoA C-acyltransferase
Similarity search - Component
Biological speciesLEISHMANIA MEXICANA (eukaryote)
MethodX-RAY DIFFRACTION / 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
DepositionNov 11, 2012Deposition 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 / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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)199,2067
Polymers196,9044
Non-polymers2,3033
Water6,720373
1
A: 3-KETOACYL-COA THIOLASE-LIKE PROTEIN
B: 3-KETOACYL-COA THIOLASE-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,9874
Polymers98,4522
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-23.9 kcal/mol
Surface area28290 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)99,2193
Polymers98,4522
Non-polymers7681
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-18.8 kcal/mol
Surface area28680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.260, 89.830, 126.240
Angle α, β, γ (deg.)90.00, 105.80, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.7778, -0.5681, 0.2688), (-0.5651, 0.4449, -0.6948), (0.2751, -0.6923, -0.6671)-5.74196, -36.802, -71.9713
2given(0.9852, 0.171, 0.008953), (0.171, -0.98, -0.1022), (-0.008704, 0.1022, -0.9947)15.0617, 31.9477, -60.8303
3given(-0.8699, 0.4426, -0.2177), (-0.4668, -0.5961, 0.6533), (0.1594, 0.6699, 0.7251)-51.7331, 11.2592, -49.953
4given(-0.8653, 0.4489, -0.2229), (-0.4776, -0.6039, 0.6381), (0.1519, 0.6587, 0.737)-51.9667, 11.0512, -49.6056
5given(0.9842, 0.177, -0.000337), (0.1763, -0.9804, -0.08776), (-0.01586, 0.08632, -0.9961)14.6696, 32.2652, -60.4454
6given(-0.9383, 0.3283, -0.1091), (0.3249, 0.7283, -0.6033), (-0.1186, -0.6015, -0.79)-69.4414, 9.96294, -9.30371

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Components

#1: Protein
3-KETOACYL-COA THIOLASE-LIKE PROTEIN / SCP2 THIOLASE


Mass: 49225.926 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEISHMANIA MEXICANA (eukaryote) / Strain: MHOM/BZ/84/BEL46
Description: THIS LEISHMANIA MEXICANA STRAIN WAS OBTAINED FROM THE INSTITUTE FOR TROPICAL MEDICINE IN ANTWERP.
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E9AW84, acetyl-CoA C-acyltransferase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE CONFLICTS EXIST AS DATABASE REFERENCE BELONGS TO A DIFFERENT STRAIN.

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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: 46.6 % / Description: NONE
Crystal growpH: 8 / Details: 100 MM TRIS PH 8.0, 200 MM NACL AND 20 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jul 23, 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
ReflectionResolution: 2.45→72.2 Å / Num. obs: 62765 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.2
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.6 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZBG

3zbg


Resolution: 2.45→121.47 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.864 / SU B: 9.65 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.793 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY THE FIRST 11 RESIDUES FROM THE N-TERMINUS ARE DISORDERED AND COULD NOT BE BUILT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2541 3195 5.1 %RANDOM
Rwork0.20868 ---
obs0.211 59546 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.565 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20.45 Å2
2--0.61 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.45→121.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12896 0 144 373 13413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01913288
X-RAY DIFFRACTIONr_bond_other_d0.0070.028907
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.97617951
X-RAY DIFFRACTIONr_angle_other_deg1.35321824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1651728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.7824.767558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.501152276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2921568
X-RAY DIFFRACTIONr_chiral_restr0.0860.21992
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214987
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022560
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
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 256 -
Rwork0.263 4161 -
obs--98.42 %

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