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Open data
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Basic information
Entry | Database: PDB / ID: 1hpu | ||||||
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Title | 5'-NUCLEOTIDASE (CLOSED FORM), COMPLEX WITH AMPCP | ||||||
![]() | 5'-NUCLEOTIDASE | ||||||
![]() | HYDROLASE / metalloenzyme / metallophosphatase / domain rotation / domain movement | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Knoefel, T. / Straeter, N. | ||||||
![]() | ![]() Title: Mechanism of hydrolysis of phosphate esters by the dimetal center of 5'-nucleotidase based on crystal structures. Authors: Knofel, T. / Strater, N. #1: ![]() 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 | ![]() | 440.5 KB | Display | ![]() |
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PDB format | ![]() | 355 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 86.3 KB | Display | |
Data in CIF | ![]() | 124.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ho5C ![]() 1hp1C ![]() 3ushS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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 % |