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Yorodumi- PDB-3zbl: Crystal structure of SCP2 thiolase from Leishmania mexicana: The ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zbl | ||||||
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Title | Crystal structure of SCP2 thiolase from Leishmania mexicana: The C123S mutant. | ||||||
Components | 3-KETOACYL-COA THIOLASE-LIKE PROTEIN | ||||||
Keywords | TRANSFERASE / COENZYME A TRANSFERASE | ||||||
Function / homology | Function and homology information propanoyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / lipid transport / peroxisome / lipid binding Similarity search - Function | ||||||
Biological species | LEISHMANIA MEXICANA (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Harijan, R.K. / Kiema, T.-R. / Weiss, M.S. / Michels, P.A.M. / Wierenga, R.K. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zbl.cif.gz | 190.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zbl.ent.gz | 150.2 KB | Display | PDB format |
PDBx/mmJSON format | 3zbl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zbl_validation.pdf.gz | 476.8 KB | Display | wwPDB validaton report |
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Full document | 3zbl_full_validation.pdf.gz | 485.7 KB | Display | |
Data in XML | 3zbl_validation.xml.gz | 39.3 KB | Display | |
Data in CIF | 3zbl_validation.cif.gz | 58.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/3zbl ftp://data.pdbj.org/pub/pdb/validation_reports/zb/3zbl | HTTPS FTP |
-Related structure data
Related structure data | 3zbgSC 3zbkC 3zbnC 4bi9C 4biaC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.3391, -0.7638, -0.5492), Vector: |
-Components
#1: Protein | Mass: 49241.926 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 | #3: Chemical | ChemComp-DMS / #4: Chemical | ChemComp-MPD / ( #5: Water | ChemComp-HOH / | Sequence details | SEQUENCE CONFLICTS EXIST AS DATABASE REFERENCE BELONGS TO A DIFFERENT STRAIN. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.1 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 100 MM MES PH6.5, 10% MME PEG 5000, 10% DMSO, 10% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Jul 20, 2012 / Details: HELIOS MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→61.1 Å / Num. obs: 87756 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 13.3 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.9→1.99 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZBG Resolution: 1.9→106.76 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.069 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. THE FIRST 13 RESIDUES FROM THE N-TERMINUS ARE DISORDERED AND COULD NOT BE BUILT.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.684 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→106.76 Å
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Refine LS restraints |
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