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Yorodumi- PDB-2vun: The Crystal Structure of Enamidase at 1.9 A Resolution - A new Me... -
+Open data
-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 | ||||||
Components | ENAMIDASE | ||||||
Keywords | HYDROLASE / NICOTINATE DEGRADATION / BINUCLEAR METAL CENTER / AMIDOHYDROLASES / STEREOSPECIFICITY | ||||||
Function / homology | Function and homology information enamidase / enamidase activity / nicotinate catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | EUBACTERIUM BARKERI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.89 Å | ||||||
Authors | Kress, D. / Alhapel, A. / Pierik, A.J. / Essen, L.-O. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vun.cif.gz | 299.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vun.ent.gz | 254 KB | Display | PDB format |
PDBx/mmJSON format | 2vun.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vu/2vun ftp://data.pdbj.org/pub/pdb/validation_reports/vu/2vun | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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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.) EUBACTERIUM BARKERI (bacteria) / Plasmid: PPR-IBA2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0QLE9, enamidase |
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-Non-polymers , 5 types, 1252 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MAD 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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