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Yorodumi- PDB-4m2k: Crystal structure of PLP-dependent cyclase OrfR in complex with PLP -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m2k | ||||||
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Title | Crystal structure of PLP-dependent cyclase OrfR in complex with PLP | ||||||
Components | Aminotransferase | ||||||
Keywords | TRANSFERASE / cyclase / PLP binding | ||||||
Function / homology | Function and homology information Lyases; Carbon-nitrogen lyases; Amidine-lyases / transaminase activity / biosynthetic process / pyridoxal phosphate binding / lyase activity Similarity search - Function | ||||||
Biological species | Streptomyces lavendulae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Chang, C.Y. / Liu, Y.C. / Lyu, S.Y. / Wu, C.C. / Li, T.L. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014 Title: Biosynthesis of streptolidine involved two unexpected intermediates produced by a dihydroxylase and a cyclase through unusual mechanisms. Authors: Chang, C.Y. / Lyu, S.Y. / Liu, Y.C. / Hsu, N.S. / Wu, C.C. / Tang, C.F. / Lin, K.H. / Ho, J.Y. / Wu, C.J. / Tsai, M.D. / Li, T.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m2k.cif.gz | 93.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m2k.ent.gz | 69.5 KB | Display | PDB format |
PDBx/mmJSON format | 4m2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4m2k_validation.pdf.gz | 449.3 KB | Display | wwPDB validaton report |
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Full document | 4m2k_full_validation.pdf.gz | 453.3 KB | Display | |
Data in XML | 4m2k_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 4m2k_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/4m2k ftp://data.pdbj.org/pub/pdb/validation_reports/m2/4m2k | HTTPS FTP |
-Related structure data
Related structure data | 4m23C 4m25C 4m26C 4m27C 4m2cC 4m2eC 4m2fC 4m2gC 4m2iC 4m2jSC 4m2mC 4ne0C 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: 43720.285 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces lavendulae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: G9MBV4 |
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#2: Chemical | ChemComp-PLP / |
#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: 2.97 Å3/Da / Density % sol: 58.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: 100mM Bis-Tris propane, 1M ammonium citrate tribasic, pH 7.0, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 23, 2012 |
Radiation | Monochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→30 Å / Num. all: 35604 / Num. obs: 33773 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.99→2.06 Å / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4M2J Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.925 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.199 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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