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Yorodumi- PDB-3r0z: Crystal structure of apo D-serine deaminase from Salmonella typhi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3r0z | ||||||
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Title | Crystal structure of apo D-serine deaminase from Salmonella typhimurium | ||||||
Components | D-serine dehydratase | ||||||
Keywords | LYASE / Foldtype 2 family of PLP-dependent enzymes / alpha / beta elimination of D-serine | ||||||
Function / homology | Function and homology information D-serine ammonia-lyase / D-serine ammonia-lyase activity / D-serine catabolic process / hydro-lyase activity / isoleucine biosynthetic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Bharath, S.R. / Shveta, B. / Savithri, H.S. / Murthy, M.R.N. | ||||||
Citation | Journal: Febs J. / Year: 2011 Title: Crystal structures of open and closed forms of D-serine deaminase from Salmonella typhimurium - implications on substrate specificity and catalysis Authors: Bharath, S.R. / Bisht, S. / Savithri, H.S. / Murthy, M.R.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r0z.cif.gz | 96.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r0z.ent.gz | 73.2 KB | Display | PDB format |
PDBx/mmJSON format | 3r0z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3r0z_validation.pdf.gz | 451.4 KB | Display | wwPDB validaton report |
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Full document | 3r0z_full_validation.pdf.gz | 456.7 KB | Display | |
Data in XML | 3r0z_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 3r0z_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/3r0z ftp://data.pdbj.org/pub/pdb/validation_reports/r0/3r0z | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 48486.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Gene: dsdA, STM3802 / Plasmid: pET21b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta / References: UniProt: Q8ZL08, D-serine ammonia-lyase | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.1 Details: 0.1M Trisodium citrate pH 6.1, 0.4M Ammonium sulphate, 0.8M Ammonium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 11, 2009 / Details: Mirror |
Radiation | Monochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→49.9 Å / Num. obs: 17806 / % possible obs: 97.1 % / Redundancy: 4.1 % / Biso Wilson estimate: 37.4 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2301 / % possible all: 87.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→45.85 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.881 / SU B: 9.895 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 27.113 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→45.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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