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Yorodumi- PDB-3edm: Crystal structure of a short chain dehydrogenase from Agrobacteri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3edm | ||||||
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Title | Crystal structure of a short chain dehydrogenase from Agrobacterium tumefaciens | ||||||
Components | Short chain dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / STRUCTURAL GENOMICS / DEHYDROGENASE / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Short chain dehydrogenase Function and homology information | ||||||
Biological species | Agrobacterium tumefaciens str. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Bonanno, J.B. / Rutter, M. / Bain, K.T. / Chang, S. / Romero, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a short chain dehydrogenase from Agrobacterium tumefaciens Authors: Bonanno, J.B. / Rutter, M. / Bain, K.T. / Chang, S. / Romero, R. / Wasserman, S. / Sauder, J.M. / 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 | 3edm.cif.gz | 166.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3edm.ent.gz | 132.3 KB | Display | PDB format |
PDBx/mmJSON format | 3edm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/3edm ftp://data.pdbj.org/pub/pdb/validation_reports/ed/3edm | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26911.521 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria) Strain: C58 / Gene: AGR_L_3556, Atu3026 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9CEK0 #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: 2.37 Å3/Da / Density % sol: 48.14 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 7 Details: 22% PEG 3350, 200mM sodium formate, pH 7.0, Vapor diffusion, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.97958 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 28, 2008 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97958 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→43.783 Å / Num. all: 46266 / Num. obs: 46266 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 4.5 / Num. measured all: 54360 / Num. unique all: 6669 / Rsym value: 0.472 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.181 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.776 / SU B: 6.627 / SU ML: 0.163 / SU R Cruickshank DPI: 0.273 / SU Rfree: 0.233 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.273 / ESU R Free: 0.233 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.01 Å2 / Biso mean: 35.109 Å2 / Biso min: 18.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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