+Open data
-Basic information
Entry | Database: PDB / ID: 1hpu | ||||||
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Title | 5'-NUCLEOTIDASE (CLOSED FORM), COMPLEX WITH AMPCP | ||||||
Components | 5'-NUCLEOTIDASE | ||||||
Keywords | HYDROLASE / metalloenzyme / metallophosphatase / domain rotation / 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: 1.85 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 | 1hpu.cif.gz | 440.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hpu.ent.gz | 355 KB | Display | PDB format |
PDBx/mmJSON format | 1hpu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/1hpu ftp://data.pdbj.org/pub/pdb/validation_reports/hp/1hpu | HTTPS FTP |
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-Related structure data
Related structure data | 1ho5C 1hp1C 3ushS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 58277.598 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: USHA / Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / Strain (production host): DS956 References: UniProt: P07024, 5'-nucleotidase, UDP-sugar diphosphatase #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-A12 / #4: 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: 2.66 Å3/Da / Density % sol: 53.67 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: sodium citrate, lithium chloride, manganese chloride, alpha,beta-methylene-ADP, PEG monomethylether 5000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
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: BW7B / Wavelength: 0.8445 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 20, 1999 |
Radiation | Monochromator: BENT SINGLE-CRYSTAL GERMANIUM TRIANGULAR MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8445 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. all: 203784 / Num. obs: 203784 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.85→1.92 Å / Rmerge(I) obs: 0.39 / % possible all: 93.2 |
Reflection | *PLUS |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ush Resolution: 1.85→28.59 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1816055.08 / 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: 44.81 Å2 / ksol: 0.3524 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→28.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.019 / 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 % reflection Rfree: 0.9 % |