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Yorodumi- PDB-3t4x: Short chain dehydrogenase/reductase family oxidoreductase from Ba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t4x | ||||||
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Title | Short chain dehydrogenase/reductase family oxidoreductase from Bacillus anthracis str. Ames Ancestor | ||||||
Components | Oxidoreductase, short chain dehydrogenase/reductase family | ||||||
Keywords | OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Oxidoreductase, short chain dehydrogenase/reductase family / Oxidoreductase, short chain dehydrogenase/reductase family Function and homology information | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å | ||||||
Authors | Filippova, E.V. / Wawrzak, Z. / Skarina, T. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: Short chain dehydrogenase/reductase family oxidoreductase from Bacillus anthracis str. 'Ames Ancestor' Authors: Filippova, E.V. / Wawrzak, Z. / Skarina, T. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t4x.cif.gz | 214.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t4x.ent.gz | 182.8 KB | Display | PDB format |
PDBx/mmJSON format | 3t4x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t4x_validation.pdf.gz | 437.9 KB | Display | wwPDB validaton report |
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Full document | 3t4x_full_validation.pdf.gz | 451.5 KB | Display | |
Data in XML | 3t4x_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 3t4x_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t4/3t4x ftp://data.pdbj.org/pub/pdb/validation_reports/t4/3t4x | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 29990.797 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: BAS3188, BA_3440, GBAA_3440 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q81MX9, UniProt: A0A384KDK1*PLUS #2: 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: 2.88 Å3/Da / Density % sol: 57.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Tacsimate 60%,NaCl 0.2M, CaAcetate 5mM, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.06885 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2011 / Details: MIRRORS |
Radiation | Monochromator: SE {111} CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.06885 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 17682 / Num. obs: 17682 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 89.9 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 19.04 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1572 / % possible all: 89.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 34.481 / SU ML: 0.305 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.943 / ESU R Free: 0.372 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 92.352 Å2
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Refine analyze | Luzzati coordinate error obs: 0.5 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 2017 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.8→2.867 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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