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Yorodumi- PDB-1qjc: Phosphopantetheine Adenylyltransferase from Escherichia coli in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qjc | ||||||
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Title | Phosphopantetheine Adenylyltransferase from Escherichia coli in complex with 4'-phosphopantetheine | ||||||
Components | PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE | ||||||
Keywords | COENZYME A BIOSYNTHESIS / TRANSFERASE / NUCLEOTIDYLTRANSFERASE | ||||||
Function / homology | Function and homology information pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | Izard, T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: The Crystal Structures of Phosphopantetheine Adenylyltransferase with Bound Substrates Reveal the Enzyme'S Catalytic Mechanism Authors: Izard, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qjc.cif.gz | 80.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qjc.ent.gz | 61.1 KB | Display | PDB format |
PDBx/mmJSON format | 1qjc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qjc_validation.pdf.gz | 436.2 KB | Display | wwPDB validaton report |
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Full document | 1qjc_full_validation.pdf.gz | 441.8 KB | Display | |
Data in XML | 1qjc_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 1qjc_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/1qjc ftp://data.pdbj.org/pub/pdb/validation_reports/qj/1qjc | HTTPS FTP |
-Related structure data
Related structure data | 1gn8C 1b6tS S: Starting model for refinement 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.066398, 0.128795, -0.989446), Vector: Details | BIOLOGICAL_UNIT: HOMOHEXAMER | |
-Components
#1: Protein | Mass: 17728.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) References: UniProt: P23875, UniProt: P0A6I6*PLUS, pantetheine-phosphate adenylyltransferase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-PNS / | #4: Water | ChemComp-HOH / | Compound details | FUNCTION: REVERSIBLY TRANSFERS AN ADENYLYL GROUP FROM ATP TO 4'- PHOSPHOPANTETHEINE, YIELDING ...FUNCTION: REVERSIBLY | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57 % |
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Crystal grow | pH: 5 / Details: pH 5.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.54 |
Detector | Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 33838 / % possible obs: 86.3 % / Observed criterion σ(I): 1 / Redundancy: 20.02 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 44.2 |
Reflection shell | Resolution: 1.8→1.91 Å / Rmerge(I) obs: 0.409 / % possible all: 51.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1B6T Resolution: 1.63→67.67 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3212744.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.226 Å2 / ksol: 0.363602 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.63→67.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.63→1.73 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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