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Yorodumi- PDB-1t8s: Crystal Structure of E.coli AMP Nucleosidase complexed with formi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t8s | ||||||
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Title | Crystal Structure of E.coli AMP Nucleosidase complexed with formicin 5'-monophosphate | ||||||
Components | AMP nucleosidase | ||||||
Keywords | HYDROLASE / ALPHA-BETA-ALPHA SANDWICH / ALPHA-BETA FOLD | ||||||
Function / homology | Function and homology information AMP nucleosidase / AMP nucleosidase activity / nucleoside metabolic process / AMP salvage / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Zhang, Y. / Cottet, S.E. / Ealick, S.E. | ||||||
Citation | Journal: STRUCTURE / Year: 2004 Title: Structure of Escherichia coli AMP Nucleosidase Reveals Similarity to Nucleoside Phosphorylases Authors: Zhang, Y. / Cottet, S.E. / Ealick, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t8s.cif.gz | 520.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t8s.ent.gz | 442.2 KB | Display | PDB format |
PDBx/mmJSON format | 1t8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1t8s_validation.pdf.gz | 708.5 KB | Display | wwPDB validaton report |
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Full document | 1t8s_full_validation.pdf.gz | 780.1 KB | Display | |
Data in XML | 1t8s_validation.xml.gz | 59.2 KB | Display | |
Data in CIF | 1t8s_validation.cif.gz | 86.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/1t8s ftp://data.pdbj.org/pub/pdb/validation_reports/t8/1t8s | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 54244.273 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: AMN, B1982, Z3139, ECS2779 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) References: UniProt: P15272, UniProt: P0AE12*PLUS, AMP nucleosidase #2: Chemical | ChemComp-FMP / #3: 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: 2.72 Å3/Da / Density % sol: 54.7 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: ammonium formate, sodium chloride, sodium citrate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.9778 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 4, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 104304 / Num. obs: 100422 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 49.5 Å2 / Rsym value: 0.118 / Net I/σ(I): 37.9 |
Reflection shell | Resolution: 2.6→2.76 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 4 / Rsym value: 0.384 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→36.75 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 564873.99 / 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: 35.5524 Å2 / ksol: 0.309109 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→36.75 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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