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Yorodumi- PDB-1ho5: 5'-NUCLEOTIDASE (E. COLI) IN COMPLEX WITH ADENOSINE AND PHOSPHATE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ho5 | ||||||
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Title | 5'-NUCLEOTIDASE (E. COLI) IN COMPLEX WITH ADENOSINE AND PHOSPHATE | ||||||
Components | 5'-NUCLEOTIDASE | ||||||
Keywords | HYDROLASE / metalloprotein / domain movement | ||||||
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: 2.1 Å | ||||||
Authors | Knoefel, T. / Straeter, N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Mechanism of hydrolysis of phosphate esters by the dimetal center of 5'-nucleotidase based on crystal structures. Authors: Knofel, T. / Strater, 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 | 1ho5.cif.gz | 224.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ho5.ent.gz | 176.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ho5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/1ho5 ftp://data.pdbj.org/pub/pdb/validation_reports/ho/1ho5 | HTTPS FTP |
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-Related structure data
Related structure data | 1hp1C 1hpuC 1ushS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 58277.598 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: USHA / Production host: Escherichia coli (E. coli) / Strain (production host): DS956 References: UniProt: P07024, 5'-nucleotidase, UDP-sugar diphosphatase #2: Chemical | ChemComp-MN / #3: Chemical | #4: Chemical | #5: 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: 2.52 Å3/Da / Density % sol: 51.09 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: sodium citrate, lithium chloride, potassium phosphate, adenosine, manganese chloride, PEG monomethylether 5000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / Details: Knofel, T., (2001) J.Mol.Biol., 309, 255. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: X11 / Wavelength: 0.9116 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 25, 1999 |
Radiation | Monochromator: bent single-crystal germanium triangular monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9116 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 69235 / Num. obs: 69235 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.298 / % possible all: 97.2 |
Reflection | *PLUS |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ush Resolution: 2.1→29.56 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2757655.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.2 Å2 / ksol: 0.3247 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→29.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.324 / Rfactor Rwork: 0.269 |