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Yorodumi- PDB-1b6t: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE IN COMPLEX WITH 3'-DEPHOSP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b6t | ||||||
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Title | PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE IN COMPLEX WITH 3'-DEPHOSPHO-COA FROM ESCHERICHIA COLI | ||||||
Components | PROTEIN (PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE) | ||||||
Keywords | TRANSFERASE / COENZYME A BIOSYNTHESIS | ||||||
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 / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Izard, T. | ||||||
Citation | Journal: EMBO J. / Year: 1999 Title: The crystal structure of a novel bacterial adenylyltransferase reveals half of sites reactivity. Authors: Izard, T. / Geerlof, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b6t.cif.gz | 81.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b6t.ent.gz | 62 KB | Display | PDB format |
PDBx/mmJSON format | 1b6t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/1b6t ftp://data.pdbj.org/pub/pdb/validation_reports/b6/1b6t | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: |
-Components
#1: Protein | Mass: 17859.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) References: UniProt: P0A6I6, pantetheine-phosphate adenylyltransferase #2: Chemical | #3: Chemical | ChemComp-COD / | #4: Water | ChemComp-HOH / | |
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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: 0.57 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 / Details: pH 5. | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 57 % | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
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: NSLS / Beamline: X12C / Wavelength: 0.978418,0.978668 ,0.95 | ||||||||||||
Detector | Type: BRANDEIS / Detector: CCD / Date: Jul 15, 1998 / Details: MIRRORS | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→20 Å / Num. obs: 48585 / % possible obs: 0.994 % / Observed criterion σ(I): 1 / Redundancy: 14 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 21.7 | ||||||||||||
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.239 / % possible all: 0.958 | ||||||||||||
Reflection | *PLUS Lowest resolution: 100 Å / Num. obs: 36339 / % possible obs: 94.7 % / Redundancy: 15.1 % / Num. measured all: 547185 | ||||||||||||
Reflection shell | *PLUS % possible obs: 95.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→23.96 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3664358.98 / 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: 68.3718 Å2 / ksol: 0.406625 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→23.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 25.8 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.327 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.275 |