+Open data
-Basic information
Entry | Database: PDB / ID: 5oo4 | ||||||
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Title | Streptomyces PAC13 with uridine | ||||||
Components | Putative cupin_2 domain-containing isomerase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Pac13 / Dehydratase / Pacidamycin | ||||||
Function / homology | RmlC-like cupin domain superfamily / isomerase activity / RmlC-like jelly roll fold / URIDINE / Putative cupin_2 domain-containing isomerase Function and homology information | ||||||
Biological species | Streptomyces coeruleorubidus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Chung, C. / Michailidou, F. | ||||||
Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2017 Title: Pac13 is a Small, Monomeric Dehydratase that Mediates the Formation of the 3'-Deoxy Nucleoside of Pacidamycins. Authors: Michailidou, F. / Chung, C.W. / Brown, M.J.B. / Bent, A.F. / Naismith, J.H. / Leavens, W.J. / Lynn, S.M. / Sharma, S.V. / Goss, R.J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oo4.cif.gz | 46.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oo4.ent.gz | 31.8 KB | Display | PDB format |
PDBx/mmJSON format | 5oo4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5oo4_validation.pdf.gz | 440.7 KB | Display | wwPDB validaton report |
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Full document | 5oo4_full_validation.pdf.gz | 440.9 KB | Display | |
Data in XML | 5oo4_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 5oo4_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/5oo4 ftp://data.pdbj.org/pub/pdb/validation_reports/oo/5oo4 | HTTPS FTP |
-Related structure data
Related structure data | 5njnC 5njoC 5oo5C 5oo8C 5oo9C 5ooaC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14111.614 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coeruleorubidus (bacteria) Gene: pac13, pacM / Production host: Escherichia coli (E. coli) / References: UniProt: E2EKP5 |
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#2: Chemical | ChemComp-URI / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 15% PEG3350,0.2M NaAc,0.09MBis-Tris pH6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Jul 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→28.93 Å / Num. obs: 17785 / % possible obs: 92.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 13.848 Å2 / Net I/σ(I): 27.4 |
Reflection shell | Resolution: 1.6→1.71 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.108 / Mean I/σ(I) obs: 7 / Num. unique obs: 2281 / % possible all: 67.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→28.56 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.417 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.086 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.848 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→28.56 Å
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Refine LS restraints |
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