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- PDB-3f3m: Six Crystal Structures of Two Phosphopantetheine Adenylyltransfer... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3f3m | ||||||
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Title | Six Crystal Structures of Two Phosphopantetheine Adenylyltransferases Reveal an Alternative Ligand Binding Mode and an Associated Structural Change | ||||||
![]() | Phosphopantetheine adenylyltransferase | ||||||
![]() | TRANSFERASE / Phosphopantetheine adenylyltransferase / PPAT / Coenzyme A biosynthetic pathway / Coenzyme A biosynthesis / Nucleotidyltransferase | ||||||
Function / homology | ![]() pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lee, H.H. / Yoon, H.J. / Suh, S.W. | ||||||
![]() | ![]() Title: The structure of Staphylococcus aureus phosphopantetheine adenylyltransferase in complex with 3'-phosphoadenosine 5'-phosphosulfate reveals a new ligand-binding mode Authors: Lee, H.H. / Yoon, H.J. / Kang, J.Y. / Park, J.H. / Kim, D.J. / Choi, K.H. / Lee, S.K. / Song, J. / Kim, H.J. / Suh, S.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 46.6 KB | Display | ![]() |
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PDB format | ![]() | 32.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 789.1 KB | Display | ![]() |
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Full document | ![]() | 791 KB | Display | |
Data in XML | ![]() | 5.9 KB | Display | |
Data in CIF | ![]() | 7.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1b6tS ![]() 3f3i ![]() 3f3j ![]() 3f3l ![]() 3f3n ![]() 3f3o S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19468.309 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P63820, pantetheine-phosphate adenylyltransferase |
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#2: Chemical | ChemComp-PPS / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.05 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100mM imidazone, 0.9-1.2M potassium/sodium tartrate, 0.2M NaCl, pH8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 24, 2004 / Details: Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 12227 / % possible obs: 98.8 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 5.6 / Num. unique all: 1161 / % possible all: 93.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1B6T Resolution: 2.4→30 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
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Solvent computation | Bsol: 34.131 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 95.89 Å2 / Biso mean: 31.96 Å2 / Biso min: 5.75 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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Xplor file |
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