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- PDB-3zbg: Crystal structure of wild-type SCP2 thiolase from Leishmania mexi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zbg | ||||||
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Title | Crystal structure of wild-type SCP2 thiolase from Leishmania mexicana at 1.85 A | ||||||
![]() | 3-KETOACYL-COA THIOLASE-LIKE PROTEIN | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() propanoyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / lipid transport / peroxisome / lipid binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Harijan, R.K. / Kiema, T.-R. / Weiss, M.S. / Michels, P.A.M. / Wierenga, R.K. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 189.8 KB | Display | ![]() |
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PDB format | ![]() | 150.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 482.3 KB | Display | ![]() |
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Full document | ![]() | 493.3 KB | Display | |
Data in XML | ![]() | 39.8 KB | Display | |
Data in CIF | ![]() | 57.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zbkC ![]() 3zblC ![]() 3zbnC ![]() 4bi9C ![]() 4biaC ![]() 1afwS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.4947, 0.2912, -0.8189), Vector: |
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Components
#1: Protein | Mass: 49305.988 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: THE NUCLEOPHILIC CYSTEINE (CYS123) IS PARTIALLY OXIDIZED TO CYSTEINE SULFONATE. Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-DMS / #3: Chemical | ChemComp-MPD / ( #4: 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.6 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 100 MM MES PH6.5, 10% MME PEG5000, 10% DMSO, 10% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 19, 2011 / Details: MIRRORS |
Radiation | Monochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→31.74 Å / Num. obs: 95952 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AFW Resolution: 1.85→105.87 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.541 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. THE FIRST 10 RESIDUES 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: 22.865 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→105.87 Å
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Refine LS restraints |
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