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- PDB-2xly: Structural and Mechanistic Analysis of the Magnesium-Independent ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xly | ||||||
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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 / Aromatic prenyltransferase, CloQ-type / Prenyltransferase-like superfamily / Aromatic prenyltransferase Orf2 / Aromatic prenyltransferase / transferase activity, transferring alkyl or aryl (other than methyl) groups / prenyltransferase activity / antibiotic biosynthetic process / 4-hydroxyphenylpyruvate 3-dimethylallyltransferase![]() | ||||||
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 | ![]() | 72.2 KB | Display | ![]() |
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PDB format | ![]() | 53.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.8 KB | Display | ![]() |
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Full document | ![]() | 433 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 16.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xlqSC ![]() 2xm5C ![]() 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: 35953.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: LIGAND-FREE FORM Source: (gene. exp.) ![]() Plasmid: CLOQ-PET28A / Production host: ![]() ![]() |
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Sequence details | THERE IS AN ADDITIONAL TRIPEPTIDE (WITH SEQUENCE GLY-SER- HIS) AT THE N-TERMINUS LEFT OVER AFTER ...THERE IS 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 AT 10 MG PER ML WAS MIXED WITH AN EQUAL VOLUME OF 3 M SODIUM FORMATE, 2 MM DITHIOTHREITOL IN 100 MM HEPES BUFFER AT PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 19, 2008 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→23.24 Å / Num. obs: 8365 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 13.12 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 3.1→3.27 Å / Redundancy: 12.19 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.73 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2XLQ Resolution: 3.1→23.24 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.883 / SU B: 18.226 / SU ML: 0.302 / Cross valid method: THROUGHOUT / ESU R Free: 0.409 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.9 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→23.24 Å
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Refine LS restraints |
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