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Yorodumi- PDB-1oie: 5'-Nucleotidase (E. coli) with an Engineered Disulfide Bridge (S2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oie | ||||||
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Title | 5'-Nucleotidase (E. coli) with an Engineered Disulfide Bridge (S228C, P513C) | ||||||
Components | PROTEIN USHA | ||||||
Keywords | HYDROLASE / METALLOPROTEIN / DOMAIN MOVEMENT / DISULFIDE ENGINEERING / CONFORMATIONAL TRAPPING / PERIPLASMIC | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | ||||||
Authors | Schultz-Heienbrok, R. / Maier, T. / Straeter, N. | ||||||
Citation | Journal: Protein Sci. / Year: 2004 Title: Trapping a 96 Degree Domain Rotation in Two Distinct Conformations by Engineered Disulfide Bridges Authors: Schultz-Heienbrok, R. / Maier, T. / Straeter, N. #1: Journal: J.Mol.Biol. / Year: 2001 Title: E. Coli 5'-Nucleotidase Undergoes a Hinge-Bending Domain Rotation Resembling a Ball-and-Socket Motion Authors: Knoefel, T. / Straeter, N. #2: Journal: Nat.Struct.Biol. / Year: 1999 Title: X-Ray Structure of the Escherichia Coli Periplasmic 5'-Nucleotidase Containing a Dimetal Catalytic Site Authors: Knoefel, T. / Straeter, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oie.cif.gz | 124.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oie.ent.gz | 93.8 KB | Display | PDB format |
PDBx/mmJSON format | 1oie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/1oie ftp://data.pdbj.org/pub/pdb/validation_reports/oi/1oie | HTTPS FTP |
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-Related structure data
Related structure data | 1oi8C 1oidC 1hp1S S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 59257.703 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) Description: DISULFIDE CROSSLINK BETWEEN N- AND C-TERMINAL DOMAINS Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ER2566 References: UniProt: P07024, 5'-nucleotidase, UDP-sugar diphosphatase | ||
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#2: Chemical | ChemComp-NI / | ||
#3: Water | ChemComp-HOH / | ||
Compound details | CHAIN A ENGINEEREDSequence details | ADDITIONAL | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.3 % |
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Crystal grow | pH: 6.5 / Details: 2.1 MALONATE PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.54179 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 2003 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→20 Å / Num. obs: 193519 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6.96 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 28.4 |
Reflection shell | Resolution: 2.33→2.41 Å / Redundancy: 6.84 % / Rmerge(I) obs: 0.165 / Mean I/σ(I) obs: 11.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HP1 Resolution: 2.33→74.54 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.903 / SU B: 5.303 / SU ML: 0.131 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.94 Å2
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Refinement step | Cycle: LAST / Resolution: 2.33→74.54 Å
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Refine LS restraints |
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