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Yorodumi- PDB-4d9b: Pyridoxamine 5' phosphate (PMP) bound form of Salmonella typhimur... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4d9b | ||||||
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Title | Pyridoxamine 5' phosphate (PMP) bound form of Salmonella typhimurium D-Cysteine desulfhydrase obtained after co-crystallization with D-cycloserine | ||||||
Components | D-cysteine desulfhydrase | ||||||
Keywords | LYASE / Fold type II PLP-dependent enzyme or tryptophan synthase beta subunit like family / PLP dependent enzyme | ||||||
Function / homology | Function and homology information D-cysteine desulfhydrase / D-amino acid metabolic process / D-cysteine desulfhydrase activity Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | ||||||
Authors | Bharath, S.R. / Shveta, B. / Rajesh, K.H. / Savithri, H.S. / Murthy, M.R.N. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Structural and Mutational Studies on Substrate Specificity and Catalysis of Salmonella typhimurium D-Cysteine Desulfhydrase. Authors: Bharath, S.R. / Bisht, S. / Harijan, R.K. / 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 | 4d9b.cif.gz | 271.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d9b.ent.gz | 218.2 KB | Display | PDB format |
PDBx/mmJSON format | 4d9b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4d9b_validation.pdf.gz | 507 KB | Display | wwPDB validaton report |
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Full document | 4d9b_full_validation.pdf.gz | 530.8 KB | Display | |
Data in XML | 4d9b_validation.xml.gz | 58.6 KB | Display | |
Data in CIF | 4d9b_validation.cif.gz | 84.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/4d9b ftp://data.pdbj.org/pub/pdb/validation_reports/d9/4d9b | HTTPS FTP |
-Related structure data
Related structure data | 4d8tSC 4d8uC 4d8wC 4d92C 4d96C 4d97C 4d99C 4d9cC 4d9eC 4d9fC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36550.727 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: dcyD, STM1953 / Plasmid: pRSET C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta / References: UniProt: Q8ZNT7, D-cysteine desulfhydrase #2: Chemical | #3: Chemical | ChemComp-PMP / #4: Chemical | ChemComp-EDO / #5: 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: 2.24 Å3/Da / Density % sol: 44.98 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: 1.5M Ammonium sulphate, 15% (v/v) ethylene glycol, 0.1M HEPES, 0.2% Benzamidine, 10mM D-Cycloserine, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 19, 2010 / Details: bent collimating mirror and torroid |
Radiation | Monochromator: Si(III) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.67→50 Å / Num. obs: 143652 / % possible obs: 96.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 33.94 |
Reflection shell | Resolution: 1.67→1.73 Å / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 3.68 / % possible all: 89.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4D8T Resolution: 1.67→39.91 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.037 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.099 / 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: 22.025 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→39.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.673→1.717 Å / Total num. of bins used: 20
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