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- PDB-1gn8: PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE IN COMPLEX WITH Mn2+ATP FR... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gn8 | ||||||
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Title | PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE IN COMPLEX WITH Mn2+ATP FROM ESCHERICHIA COLI | ||||||
![]() | PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE | ||||||
![]() | TRANSFERASE / COENZYME A BIOSYNTHESIS / NUCLEOTIDYLTRANSFERASE | ||||||
Function / homology | ![]() pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Izard, T. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.2 KB | Display | ![]() |
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PDB format | ![]() | 61.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 523.1 KB | Display | ![]() |
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Full document | ![]() | 528.9 KB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Data in CIF | ![]() | 14.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qjcC ![]() 1b6tS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17859.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P23875, UniProt: P0A6I6*PLUS, pantetheine-phosphate adenylyltransferase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 60 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 / Details: pH 5.00 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 57 % | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Izard, T., (1999) Acta Crystallog., D55, 1226. / 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: ![]() |
Detector | Type: MAC Science DIP / Detector: IMAGE PLATE / Date: Jul 21, 2000 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→20 Å / Num. obs: 35949 / % possible obs: 97.1 % / Observed criterion σ(I): 1 / Redundancy: 12.351 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.163 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.82→1.82 Å / Rmerge(I) obs: 0.495 / % possible all: 77.8 |
Reflection | *PLUS % possible obs: 96.9 % / Num. measured all: 444009 / Rmerge(I) obs: 0.107 |
Reflection shell | *PLUS % possible obs: 77.7 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PBD ENTRY 1B6T Resolution: 1.83→21.91 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.83→21.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.83→1.94 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: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 35859 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 24.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.338 |