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Yorodumi- PDB-4mzy: Crystal structure of enterococcus faecalis nicotinate phosphoribo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mzy | ||||||
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Title | Crystal structure of enterococcus faecalis nicotinate phosphoribosyltransferase with malonate and phosphate bound | ||||||
Components | NICOTINATE PHOSPHORIBOSYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / STRUCTURAL GENOMICS / PSI / ROTEIN STRUCTURE INITIATIVE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS / NYSGXRC / New York Structural Genomics Research Consortium / NYSGRC / Protein Structure Initiative | ||||||
Function / homology | Function and homology information nicotinate phosphoribosyltransferase / nicotinate phosphoribosyltransferase activity / NAD biosynthetic process / glycosyltransferase activity Similarity search - Function | ||||||
Biological species | ENTEROCOCCUS FAECALIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Patskovsky, Y. / Toro, R. / Wasserman, S.R. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Enterococcus Faecalis Nicotinate Phosphoribosyltransferase Authors: Patskovsky, Y. / Toro, R. / Wasserman, S.R. / Burley, S.K. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mzy.cif.gz | 118.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mzy.ent.gz | 91.7 KB | Display | PDB format |
PDBx/mmJSON format | 4mzy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mz/4mzy ftp://data.pdbj.org/pub/pdb/validation_reports/mz/4mzy | HTTPS FTP |
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-Related structure data
Related structure data | 2f7fSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 56600.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ENTEROCOCCUS FAECALIS (bacteria) / Strain: V583 / Gene: EF2626 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q830Y8, EC: 2.4.2.11 |
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-Non-polymers , 6 types, 192 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-FMT / | #7: 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: 2.46 Å3/Da / Density % sol: 49.75 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.4 M SODIUM MALONATE, 10% GLYCEROL, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 9, 2007 / Details: MIRRORS |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 44766 / % possible obs: 99.8 % / Observed criterion σ(I): -5 / Redundancy: 4.1 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 4 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.669 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2F7F Resolution: 1.95→25.78 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.912 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.115 / 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: 35.95 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→25.78 Å
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Refine LS restraints |
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