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Yorodumi- PDB-5b6e: Crystal Structure of cytidine monophosphate hydroxymethylase MilA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b6e | ||||||
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Title | Crystal Structure of cytidine monophosphate hydroxymethylase MilA with hmCMP | ||||||
Components | CMP 5-hydroxymethylase | ||||||
Keywords | TRANSFERASE / hydroxymethylase | ||||||
Function / homology | Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / methyltransferase activity / methylation / Chem-5HM / CMP 5-hydroxymethylase Function and homology information | ||||||
Biological species | Streptomyces rimofaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Gong, Z. / Wu, G. / He, X. | ||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Structural basis of the substrate preference towards CMP for a thymidylate synthase MilA involved in mildiomycin biosynthesis Authors: Zhao, G. / Chen, C. / Xiong, W. / Gao, T. / Deng, Z. / Wu, G. / He, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b6e.cif.gz | 255 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b6e.ent.gz | 206.6 KB | Display | PDB format |
PDBx/mmJSON format | 5b6e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/5b6e ftp://data.pdbj.org/pub/pdb/validation_reports/b6/5b6e | HTTPS FTP |
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-Related structure data
Related structure data | 5b6dC 5jnhSC 5jp9C C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 36528.031 Da / Num. of mol.: 2 / Fragment: UNP residues 5-329 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces rimofaciens (bacteria) / Gene: milA / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B4Y380 #2: Chemical | #3: 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: 2.67 Å3/Da / Density % sol: 53.85 % |
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Crystal grow | Temperature: 289 K / Method: evaporation / pH: 8.5 Details: 0.1 M sodium cacodylate trihydrate(pH 6.5), 1.4 M sodium acetate trihydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97912 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97912 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 68810 / % possible obs: 100 % / Redundancy: 11.2 % / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.8→1.86 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JNH Resolution: 1.8→49.24 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.143 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.106 / 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 max: 50.17 Å2 / Biso mean: 22.571 Å2 / Biso min: 13.82 Å2
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Refinement step | Cycle: final / Resolution: 1.8→49.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.848 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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