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- PDB-1oid: 5'-Nucleotidase (E. coli) with an Engineered Disulfide Bridge (S2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1oid | ||||||
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Title | 5'-Nucleotidase (E. coli) with an Engineered Disulfide Bridge (S228C, P513C) | ||||||
![]() | PROTEIN USHA | ||||||
![]() | HYDROLASE / METALLOPROTEIN / DOMAIN MOVEMENT / DISULFIDE ENGINEERING / UDP-SUGAR HYDROLASE / CONFORMATIONAL TRAPPING | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Schultz-Heienbrok, R. / Maier, T. / Straeter, N. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 231.7 KB | Display | ![]() |
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PDB format | ![]() | 184.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.8 KB | Display | ![]() |
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Full document | ![]() | 481.4 KB | Display | |
Data in XML | ![]() | 48.7 KB | Display | |
Data in CIF | ![]() | 71.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1oi8C ![]() 1oieC ![]() 1hp1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.999, -0.018, 0.04), Vector: |
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Components
#1: Protein | Mass: 59257.703 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Description: DISULFIDE CROSSLINK BETWEEN N- AND C-TERMINAL DOMAINS Plasmid: PET28A / Production host: ![]() ![]() References: UniProt: P07024, 5'-nucleotidase, UDP-sugar diphosphatase #2: Chemical | ChemComp-NI / | #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUES CHAINS A, B CYS 228 SER, CYS 513 PRO CATALYTIC ACTIVITY: UDP-SUGAR + H(2)O = ...ENGINEERED | Sequence details | ADDITIONAL | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: 26% PEG 400, 100 MM CACODYLATE PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
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: 2.1→20 Å / Num. obs: 194970 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 2.78 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 2.35 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.08 / % possible all: 90.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HP1 Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.927 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.17 / 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: 36.56 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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