+Open data
-Basic information
Entry | Database: PDB / ID: 6aa9 | ||||||
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Title | T166A mutant of D-Serine deaminase from Salmonella typhimurium | ||||||
Components | D-serine dehydratase | ||||||
Keywords | LYASE / Monomer / PLP bound / Salmonella typhimurium / deaminase | ||||||
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 typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Deka, G. / Bharath, S.R. / Shavithri, H.S. / Murthy, M.R.N. | ||||||
Funding support | India, 1items
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Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2017 Title: Structural studies on the decameric S. typhimurium arginine decarboxylase (ADC): Pyridoxal 5'-phosphate binding induces conformational changes Authors: Deka, G. / Bharath, S.R. / Shavithri, 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 | 6aa9.cif.gz | 96.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6aa9.ent.gz | 70.4 KB | Display | PDB format |
PDBx/mmJSON format | 6aa9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6aa9_validation.pdf.gz | 448.9 KB | Display | wwPDB validaton report |
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Full document | 6aa9_full_validation.pdf.gz | 450.2 KB | Display | |
Data in XML | 6aa9_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 6aa9_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/6aa9 ftp://data.pdbj.org/pub/pdb/validation_reports/aa/6aa9 | HTTPS FTP |
-Related structure data
Related structure data | 5xx1C 3r0zS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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
#1: Protein | Mass: 48684.965 Da / Num. of mol.: 1 / Mutation: T166A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: dsdA, STM3802 / Plasmid: pET 21b / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: Q8ZL08, D-serine ammonia-lyase |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-PO4 / |
#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: 2.43 Å3/Da / Density % sol: 49.38 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 0.8 M lithium sulfate, 0.4 M ammonium sulfate, 100 mm trisodium citrate pH 6.1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 29, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→53.2 Å / Num. obs: 13514 / % possible obs: 99.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 15.8 Å2 / CC1/2: 0.897 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.109 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 2.7→2.83 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 1791 / CC1/2: 0.904 / Rpim(I) all: 0.181 / Rrim(I) all: 0.259 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3R0Z Resolution: 2.7→53.2 Å / Cor.coef. Fo:Fc: 0.755 / Cor.coef. Fo:Fc free: 0.664 / SU B: 19.459 / SU ML: 0.423 / Cross valid method: THROUGHOUT / ESU R Free: 0.483 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.429 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→53.2 Å
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Refine LS restraints |
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