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Yorodumi- PDB-2xlq: Structural and Mechanistic Analysis of the Magnesium-Independent ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xlq | ||||||
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Title | Structural and Mechanistic Analysis of the Magnesium-Independent Aromatic Prenyltransferase CloQ from the Clorobiocin Biosynthetic Pathway | ||||||
Components | CLOQ | ||||||
Keywords | TRANSFERASE / PT-BARREL / ANTIBIOTIC BIOSYNTHESIS | ||||||
Function / homology | Function and homology information 4-hydroxyphenylpyruvate 3-dimethylallyltransferase / transferase activity, transferring alkyl or aryl (other than methyl) groups / prenyltransferase activity / antibiotic biosynthetic process Similarity search - Function | ||||||
Biological species | STREPTOMYCES ROSEOCHROMOGENES SUBSP. OSCITANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 2.22 Å | ||||||
Authors | Metzger, U. / Keller, S. / Stevenson, C.E.M. / Heide, L. / Lawson, D.M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xlq.cif.gz | 78 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xlq.ent.gz | 61.3 KB | Display | PDB format |
PDBx/mmJSON format | 2xlq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xlq_validation.pdf.gz | 449.7 KB | Display | wwPDB validaton report |
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Full document | 2xlq_full_validation.pdf.gz | 450.5 KB | Display | |
Data in XML | 2xlq_validation.xml.gz | 16 KB | Display | |
Data in CIF | 2xlq_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/2xlq ftp://data.pdbj.org/pub/pdb/validation_reports/xl/2xlq | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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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: COMPLEX WITH 4-HYDROXYPHENOLPYRUVATE Source: (gene. exp.) STREPTOMYCES ROSEOCHROMOGENES SUBSP. OSCITANS (bacteria) Plasmid: CLOQ-PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q8GHB2 | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-34H / ( | #4: Water | ChemComp-HOH / | Nonpolymer details | 4-HYDROXYPHENYLPYRUVATE: 4-HYDROXYPHENYLPYRUVATE WAS COVALENTLY LINKED THROUGH ITS C2 ATOM TO THE ...4-HYDROXYPHE | Sequence details | THERE ARE THREE ADDITIONAL RESIDUES (WITH SEQUENCE GLY-SER- HIS) AT THE N-TERMINUS LEFT OVER AFTER ...THERE ARE THREE ADDITIONAL | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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) 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: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.542 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 9, 2006 / 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: 2.21→31.86 Å / Num. obs: 22556 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 7.75 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.63 |
Reflection shell | Resolution: 2.21→2.33 Å / Redundancy: 7.36 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.57 / % possible all: 81.6 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.22→95.78 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.845 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 17.31 Å2
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Refinement step | Cycle: LAST / Resolution: 2.22→95.78 Å
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