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Yorodumi- PDB-2kg6: Solution Structure of the acetyl Actinorhodin Acyl Carrier Protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kg6 | ||||||
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Title | Solution Structure of the acetyl Actinorhodin Acyl Carrier Protein from Streptomyces coelicolor | ||||||
Components | Actinorhodin polyketide synthase acyl carrier protein | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Acyl Carrier Protein / Acetyl / Acylated / Polyketide / Actinorhodin / Antibiotic biosynthesis / Phosphopantetheine | ||||||
Function / homology | Function and homology information lipid A biosynthetic process / antibiotic biosynthetic process / acyl binding / acyl carrier activity / cytosol Similarity search - Function | ||||||
Biological species | Streptomyces coelicolor (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Crump, M.P. / Evans, S.E. / Eliza, P. / Christopher, W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Probing the Interactions of Early Polyketide Intermediates with the Actinorhodin ACP from S. coelicolor A3(2). Authors: Evans, S.E. / Williams, C. / Arthur, C.J. / Ploskon, E. / Wattana-Amorn, P. / Cox, R.J. / Crosby, J. / Willis, C.L. / Simpson, T.J. / Crump, M.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kg6.cif.gz | 563.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kg6.ent.gz | 496.9 KB | Display | PDB format |
PDBx/mmJSON format | 2kg6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kg6_validation.pdf.gz | 416.5 KB | Display | wwPDB validaton report |
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Full document | 2kg6_full_validation.pdf.gz | 529.5 KB | Display | |
Data in XML | 2kg6_validation.xml.gz | 30.4 KB | Display | |
Data in CIF | 2kg6_validation.cif.gz | 50 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/2kg6 ftp://data.pdbj.org/pub/pdb/validation_reports/kg/2kg6 | HTTPS FTP |
-Related structure data
Related structure data | 2kg8C 2kg9C 2kgaC 2kgcC 2kgdC 2kgeC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 9239.177 Da / Num. of mol.: 1 / Mutation: C17S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: SCO5089, SCBAC28G1.15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: Q02054 |
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#2: Chemical | ChemComp-SXA / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1-2 mM [U-98% 13C; U-98% 15N] Acyl Carrier Protein-1, 20 mM potassium phosphate-2, 1 mM sodium azide-3, 95% H2O/5% D2O Solvent system: 95% H2O/5% D2O | ||||||||||||||||||||||||
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Sample |
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Sample conditions | pH: 5.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: ALL STRUCTURE CALCULATIONS WERE CARRIED OUT USING THE AMBIGUOUS RESTRAINTS FOR ITERATIVE ASSIGNMENT OF NOES (ARIA) PROTOCOL VERSION 1.2. THE 20 BEST STRUCTURES (SORTED ACCORDING TO TOTAL ...Details: ALL STRUCTURE CALCULATIONS WERE CARRIED OUT USING THE AMBIGUOUS RESTRAINTS FOR ITERATIVE ASSIGNMENT OF NOES (ARIA) PROTOCOL VERSION 1.2. THE 20 BEST STRUCTURES (SORTED ACCORDING TO TOTAL ENERGY) WERE SELECTED FOR WATER REFINEMENT. WATER REFINED STRUCTURES WERE CALCULATED USING THE SLIGHTLY MODIFIED REFINEMENT SCRIPT APPLIED TO THE RECOORD DATABASE. PROCHECK AND WHATCHECK AND QUALITY INDICATORS WERE COMPARED TO THE AVERAGE VALUES FOR THE RECOORD DATABASE OF PROTEIN NMR STRUCTURES. | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |