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- PDB-2xm5: Structural and Mechanistic Analysis of the Magnesium-Independent ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xm5 | ||||||
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Title | Structural and Mechanistic Analysis of the Magnesium-Independent Aromatic Prenyltransferase CloQ from the Clorobiocin Biosynthetic Pathway | ||||||
![]() | CLOQ | ||||||
![]() | TRANSFERASE / PT-BARREL / ANTIBIOTIC BIOSYNTHESIS | ||||||
Function / homology | ![]() 4-hydroxyphenylpyruvate 3-dimethylallyltransferase / transferase activity, transferring alkyl or aryl (other than methyl) groups / prenyltransferase activity / antibiotic biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Metzger, U. / Keller, S. / Stevenson, C.E.M. / Heide, L. / Lawson, D.M. | ||||||
![]() | ![]() Title: Structure and Mechanism of the Magnesium-Independent Aromatic Prenyltransferase Cloq from the Clorobiocin Biosynthetic Pathway. Authors: Metzger, U. / Keller, S. / Stevenson, C.E.M. / Heide, L. / Lawson, D.M. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.4 KB | Display | ![]() |
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PDB format | ![]() | 63.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.2 KB | Display | ![]() |
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Full document | ![]() | 449.9 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xlqSC ![]() 2xlyC ![]() 2xm7C S: Starting model for refinement C: citing same article ( |
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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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Components
#1: Protein | Mass: 35937.531 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: C215S MUTANT SOAKED IN 4-HYDROXYPHENYL PYRUVATE. UNINTERPRETABLE RESIDUAL ELECTRON DENSITY IN ACTIVE SITE PRESUMED TO BE THIS LIGAND. Source: (gene. exp.) ![]() Plasmid: CLOQ-PET28A / Production host: ![]() ![]() | ||||||||
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#2: Chemical | ChemComp-EDO / | ||||||||
#3: Chemical | ChemComp-FMT / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | Nonpolymer details | ETHYLENE GLYCOL (EDO): ETHYLENE GLYCOL WAS USED AS A CRYOPROTECTANT FORMATE (FMT): SODIUM FORMATE ...ETHYLENE GLYCOL (EDO): ETHYLENE GLYCOL WAS USED AS A CRYOPROTEC | Sequence details | THERE ARE AN ADDITIONAL THREE RESIDUES (WITH SEQUENCE GLY-SER- HIS) AT THE N-TERMINUS LEFT OVER ...THERE ARE AN ADDITIONAL | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.6 % / Description: NONE |
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Crystal grow | Method: vapor diffusion / pH: 6.5 Details: VAPOR DIFFUSION. PROTEIN (10 MG/ML) WAS MIXED WITH AN EQUAL VOLUME OF 3 M SODIUM FORMATE, 2 MM DITHIOTHREITOL, 100 MM HEPES PH 6.5 . |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→44.09 Å / Num. obs: 39516 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14.18 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.12 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 14.47 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.43 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2XLQ Resolution: 1.85→42.83 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.945 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→42.83 Å
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Refine LS restraints |
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