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Yorodumi- PDB-1xa0: Crystal Structure of MCSG Target APC35536 from Bacillus stearothe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xa0 | ||||||
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Title | Crystal Structure of MCSG Target APC35536 from Bacillus stearothermophilus | ||||||
Components | Putative NADPH Dependent oxidoreductases | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / protein structure initiative / MCSG / PSI / Midwest Center for Structural Genomics | ||||||
Function / homology | Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Function and homology information | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å | ||||||
Authors | Brunzelle, J.S. / Sommerhalter, M. / Minasov, G. / Shuvalova, L. / Collart, F.R. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of MCSG Target APC35536 from Bacillus stearothermophilus Authors: BRUNZELLE, J.S. / SOMMERHALTER, M. / MINASOV, G. / SHUVALOVA, L. / COLLART, F.R. / ANDERSON, W.F. / Midwest Center for Structural Genomics (MCSG) | ||||||
History |
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Remark 999 | SEQUENCE The sequence of the protein has not been deposited into any sequence database. | ||||||
Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL MOLECULE FOR THE PROTEIN IS NOT KNOWN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xa0.cif.gz | 128 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xa0.ent.gz | 107.1 KB | Display | PDB format |
PDBx/mmJSON format | 1xa0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/1xa0 ftp://data.pdbj.org/pub/pdb/validation_reports/xa/1xa0 | 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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Details | Not Known |
-Components
#1: Protein | Mass: 35711.934 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 #2: Chemical | #3: Chemical | ChemComp-CL / | #4: 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: 2.9 Å3/Da / Density % sol: 57.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8.3 Details: 160mM Ammonium sulfate, pH 8.3, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 99.8 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.979 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 18, 2004 / Details: Mirror |
Radiation | Monochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→30 Å / Num. all: 28389 / Num. obs: 28389 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.085 |
Reflection shell | Resolution: 2.65→2.75 Å / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 5.1 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.904 / SU B: 14.984 / SU ML: 0.302 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.393 / 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: 36.503 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.872 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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