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Yorodumi- PDB-1qr0: CRYSTAL STRUCTURE OF THE 4'-PHOSPHOPANTETHEINYL TRANSFERASE SFP-C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qr0 | ||||||
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Title | CRYSTAL STRUCTURE OF THE 4'-PHOSPHOPANTETHEINYL TRANSFERASE SFP-COENZYME A COMPLEX | ||||||
Components | 4'-PHOSPHOPANTETHEINYL TRANSFERASE SFP | ||||||
Keywords | TRANSFERASE / PROTEIN-COENZYME A COMPLEX | ||||||
Function / homology | Function and homology information positive regulation of single-species biofilm formation / holo-[acyl-carrier-protein] synthase / lysine biosynthetic process via aminoadipic acid / holo-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å | ||||||
Authors | Reuter, K. / Mofid, R.M. / Marahiel, A.M. / Ficner, R. | ||||||
Citation | Journal: EMBO J. / Year: 1999 Title: Crystal structure of the surfactin synthetase-activating enzyme sfp: a prototype of the 4'-phosphopantetheinyl transferase superfamily. Authors: Reuter, K. / Mofid, M.R. / Marahiel, M.A. / Ficner, R. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Crystallization and preliminary crystallographic studies of Sfp: a phosphopantetheinyl transferase of modular peptide synthetases Authors: Mofid, R.M. / Ficner, R. / Marahiel, A.M. / Reuter, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qr0.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qr0.ent.gz | 49.8 KB | Display | PDB format |
PDBx/mmJSON format | 1qr0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qr0_validation.pdf.gz | 719.9 KB | Display | wwPDB validaton report |
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Full document | 1qr0_full_validation.pdf.gz | 731.8 KB | Display | |
Data in XML | 1qr0_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 1qr0_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/1qr0 ftp://data.pdbj.org/pub/pdb/validation_reports/qr/1qr0 | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: 26543.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: SFP / Plasmid: PQE60 / Gene (production host): SFP / Production host: Bacillus subtilis (bacteria) / References: UniProt: P39135 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-COA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.23 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5 Details: SODIUM FORMATE, SODIUM ACETATE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9537 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 27, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25 Å / Num. all: 28951 / Num. obs: 28951 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.234 / % possible all: 90.6 |
Reflection | *PLUS Num. measured all: 96195 |
Reflection shell | *PLUS % possible obs: 90.6 % |
-Processing
Software |
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Refinement | Resolution: 1.9→20 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.216 / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.216 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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