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Yorodumi- PDB-1tz0: Crystal Structure of Putative Antibiotic Biosythesis Monooxygenas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tz0 | ||||||
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Title | Crystal Structure of Putative Antibiotic Biosythesis Monooxygenase from Bacillus cereus | ||||||
Components | hypothetical protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein Structure Initiative / MCSG / Hypothetical Protein / Bacillus cereus / PSI / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus cereus ATCC 14579 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.84 Å | ||||||
Authors | Kim, Y. / Lezondra, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Hypothetical Protein APC24875 from Bacillus cereus Authors: Kim, Y. / Lezondra, L. / Joachimiak, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). THE AUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS NOT NECESSARILY THE CONTENT OF THE ASYMMETRIC UNIT. THEY FOUND THAT OTHER STRUCTURES, HOMOLOGOUS TO THIS STRUCTURE FORM DIMERS. THIS STRUCTURE FORMS A SIMILAR DIMER AS WELL AS AN ASYMMETRIC TRIMER WHICH SEEMS INTIMATE ENOUGH. FOR THESE REASONS AUTHORS STATE STRUCTURE AS UNKNOWN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tz0.cif.gz | 81.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tz0.ent.gz | 65.2 KB | Display | PDB format |
PDBx/mmJSON format | 1tz0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tz0_validation.pdf.gz | 462.5 KB | Display | wwPDB validaton report |
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Full document | 1tz0_full_validation.pdf.gz | 467.4 KB | Display | |
Data in XML | 1tz0_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 1tz0_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/1tz0 ftp://data.pdbj.org/pub/pdb/validation_reports/tz/1tz0 | HTTPS FTP |
-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 on special symmetry positions |
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-Components
#1: Protein | Mass: 13163.535 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Species: Bacillus cereus / Strain: ATCC 14579 / DSM 31 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q81C15 #2: Chemical | ChemComp-EDO / | #3: Chemical | ChemComp-FMT / | #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: 3.1 Å3/Da / Density % sol: 60 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: Sodium Formate, Sodium Acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793, 0.9794, 0.954 | ||||||||||||
Detector | Type: SBC-2 / Detector: CCD / Date: Mar 20, 2004 / Details: mirrors | ||||||||||||
Radiation | Monochromator: double crystal monochromator Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.84→40 Å / Num. all: 40217 / Num. obs: 38958 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 9.3 | ||||||||||||
Reflection shell | Resolution: 1.84→1.91 Å / Redundancy: 5 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3690 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.84→37.27 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.911 / SU B: 3.152 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.145 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.499 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.84→37.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.836→1.884 Å / Total num. of bins used: 20
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