+Open data
-Basic information
Entry | Database: PDB / ID: 1t8w | ||||||
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Title | Crystal Structure of E. coli AMP Nucleosidase | ||||||
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: 2.8 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 | 1t8w.cif.gz | 532.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t8w.ent.gz | 454.3 KB | Display | PDB format |
PDBx/mmJSON format | 1t8w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1t8w_validation.pdf.gz | 416.8 KB | Display | wwPDB validaton report |
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Full document | 1t8w_full_validation.pdf.gz | 503.1 KB | Display | |
Data in XML | 1t8w_validation.xml.gz | 61.8 KB | Display | |
Data in CIF | 1t8w_validation.cif.gz | 92.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/1t8w ftp://data.pdbj.org/pub/pdb/validation_reports/t8/1t8w | 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: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 64 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: ammonium formate, sodium chloride, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.8→50 Å / Num. all: 100795 / Num. obs: 95360 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 62.5 Å2 / Rsym value: 0.064 / Net I/σ(I): 28.1 | |||||||||||||||
Reflection shell | Resolution: 2.8→2.98 Å / % possible all: 85.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→25.93 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 606662.56 / 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: 43.4374 Å2 / ksol: 0.315536 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 92 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→25.93 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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