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- PDB-3zbk: Crystal structure of SCP2 thiolase from Leishmania mexicana: The ... -

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Basic information

Entry
Database: PDB / ID: 3zbk
TitleCrystal structure of SCP2 thiolase from Leishmania mexicana: The C123A mutant.
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
propanoyl-CoA C-acyltransferase
Similarity search - Component
Biological speciesLEISHMANIA MEXICANA (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionNov 10, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,18812
Polymers98,4522
Non-polymers73610
Water11,692649
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-39.8 kcal/mol
Surface area28780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.266, 123.266, 132.936
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.8328, 0.4802, -0.2756), (0.479, 0.3753, -0.7935), (-0.2776, -0.7928, -0.5425)
Vector: 61.106, -35.5722, -24.596)

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Components

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


Mass: 49225.926 Da / Num. of mol.: 2 / 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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 649 / 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: 3.1 Å3/Da / Density % sol: 60.4 % / Description: NONE
Crystal growpH: 6.5
Details: 100 MM MES PH6.5, 10% MME PEG 5000, 10% DMSO, 10% MPD

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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 21, 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: 1.9→61.6 Å / Num. obs: 89877 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 15.5 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 14.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 4.1 / % possible all: 100

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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: 1.9→106.75 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.898 / SU B: 3.927 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.145 / 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
Rfree0.25888 4512 5 %RANDOM
Rwork0.22053 ---
obs0.22244 85194 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.445 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.26 Å20 Å2
2--0.51 Å20 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.9→106.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6448 0 38 649 7135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0196610
X-RAY DIFFRACTIONr_bond_other_d0.0060.024431
X-RAY DIFFRACTIONr_angle_refined_deg1.8271.9678915
X-RAY DIFFRACTIONr_angle_other_deg1.38310860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5895868
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.78724.804281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.673151141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8881534
X-RAY DIFFRACTIONr_chiral_restr0.1160.2998
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027475
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021267
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 340 -
Rwork0.38 6239 -
obs--100 %

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