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Yorodumi- PDB-3zbn: Crystal structure of SCP2 thiolase from Leishmania mexicana. Comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zbn | ||||||
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Title | Crystal structure of SCP2 thiolase from Leishmania mexicana. Complex of the C123A mutant with Coenzyme A. | ||||||
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: 2.45 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 | 3zbn.cif.gz | 333.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zbn.ent.gz | 272.3 KB | Display | PDB format |
PDBx/mmJSON format | 3zbn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zbn_validation.pdf.gz | 1017.9 KB | Display | wwPDB validaton report |
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Full document | 3zbn_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3zbn_validation.xml.gz | 64.9 KB | Display | |
Data in CIF | 3zbn_validation.cif.gz | 89.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/3zbn ftp://data.pdbj.org/pub/pdb/validation_reports/zb/3zbn | HTTPS FTP |
-Related structure data
Related structure data | 3zbgSC 3zbkC 3zblC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | 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 | #3: 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: 2.3 Å3/Da / Density % sol: 46.6 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 100 MM TRIS PH 8.0, 200 MM NACL AND 20 % PEG 4000 |
-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 23, 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: 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 shell | Resolution: 2.45→2.55 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.6 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 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.
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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: 16.565 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→121.47 Å
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Refine LS restraints |
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