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- PDB-2vun: The Crystal Structure of Enamidase at 1.9 A Resolution - A new Me... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vun | ||||||
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Title | The Crystal Structure of Enamidase at 1.9 A Resolution - A new Member of the Amidohydrolase Superfamily | ||||||
![]() | ENAMIDASE | ||||||
![]() | HYDROLASE / NICOTINATE DEGRADATION / BINUCLEAR METAL CENTER / AMIDOHYDROLASES / STEREOSPECIFICITY | ||||||
Function / homology | ![]() enamidase / enamidase activity / nicotinate catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kress, D. / Alhapel, A. / Pierik, A.J. / Essen, L.-O. | ||||||
![]() | ![]() Title: The Crystal Structure of Enamidase: A Bifunctional Enzyme of the Nicotinate Catabolism. Authors: Kress, D. / Alhapel, A. / Pierik, A.J. / Essen, L.-O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 304.1 KB | Display | ![]() |
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PDB format | ![]() | 248.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468 KB | Display | ![]() |
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Full document | ![]() | 482.5 KB | Display | |
Data in XML | ![]() | 66.4 KB | Display | |
Data in CIF | ![]() | 96.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 39965.645 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 1252 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-FE / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.41 % / Description: NONE |
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Crystal grow | pH: 7 Details: 0.1 M TRIS/HCL PH 7.0, 17.5 W/V-% PEG8000, 0.2 M AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 1, 2005 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→39 Å / Num. obs: 148870 / % possible obs: 99 % / Observed criterion σ(I): 2.5 / Redundancy: 3.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.89→1.94 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.9 / % possible all: 91 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 1.89→107.83 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.563 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.11 / 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: 25.08 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→107.83 Å
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Refine LS restraints |
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