+Open data
-Basic information
Entry | Database: PDB / ID: 1ush | ||||||
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Title | 5'-NUCLEOTIDASE FROM E. COLI | ||||||
Components | 5'-NUCLEOTIDASE | ||||||
Keywords | HYDROLASE / 5'-NUCLEOTIDASE / UDP-SUGAR HYDROLASE / PHOSPHATASE / HYDROLASE (PHOSPHORIC MONOESTER) / PERIPLASMIC PROTEIN | ||||||
Function / homology | Function and homology information UDP-sugar diphosphatase / UDP-sugar diphosphatase activity / nucleotide catabolic process / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / outer membrane-bounded periplasmic space / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Knofel, T. / Strater, N. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1999 Title: X-ray structure of the Escherichia coli periplasmic 5'-nucleotidase containing a dimetal catalytic site. Authors: Knofel, T. / Strater, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ush.cif.gz | 128 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ush.ent.gz | 97 KB | Display | PDB format |
PDBx/mmJSON format | 1ush.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/us/1ush ftp://data.pdbj.org/pub/pdb/validation_reports/us/1ush | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 60894.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: COMPLEX WITH CARBONATE / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: USHA / Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / References: UniProt: P07024, 5'-nucleotidase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CO3 / | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.6 / Details: pH 6.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.981 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1998 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.981 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→30 Å / Num. obs: 68495 / % possible obs: 98.4 % / Redundancy: 2.7 % / Biso Wilson estimate: 13.8 Å2 / Rsym value: 0.035 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.73→1.79 Å / Redundancy: 2.9 % / Rsym value: 0.13 / % possible all: 93.6 |
Reflection | *PLUS Rmerge(I) obs: 0.035 |
Reflection shell | *PLUS % possible obs: 93.6 % / Rmerge(I) obs: 0.13 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5'-NUCLEOTIDASE FROM E. COLI (ORTHORHOMBIC CRYSTAL FORM) Resolution: 1.73→8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 15.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.73→8 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: UNRESTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.73→1.81 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.84 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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