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Yorodumi- PDB-4hh4: Structure of the CcbJ Methyltransferase from Streptomyces caelestis -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hh4 | ||||||
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Title | Structure of the CcbJ Methyltransferase from Streptomyces caelestis | ||||||
Components | CcbJ | ||||||
Keywords | TRANSFERASE / S-adenosyl-L-methionine-dependent methyltransferase / Methyltransferase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces caelestis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Bauer, J.A. / Ondrovicova, G. / Kutejova, E. / Janata, J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structure and possible mechanism of the CcbJ methyltransferase from Streptomyces caelestis. Authors: Bauer, J. / Ondrovicova, G. / Najmanova, L. / Pevala, V. / Kamenik, Z. / Kostan, J. / Janata, J. / Kutejova, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hh4.cif.gz | 611.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hh4.ent.gz | 506 KB | Display | PDB format |
PDBx/mmJSON format | 4hh4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hh4_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 4hh4_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 4hh4_validation.xml.gz | 57 KB | Display | |
Data in CIF | 4hh4_validation.cif.gz | 76.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/4hh4 ftp://data.pdbj.org/pub/pdb/validation_reports/hh/4hh4 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS ensembles :
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 30051.688 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces caelestis (bacteria) / Gene: ccbJ / Plasmid: pET 28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: E9JES0 |
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-Non-polymers , 5 types, 140 molecules
#2: Chemical | ChemComp-SAH / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-EPE / | #6: 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: 3.39 Å3/Da / Density % sol: 63.76 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Na HEPES pH 7.5, 1.3 M Li2SO4.H2O, 10% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97549 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2009 / Details: Pd-coated toroidal mirror (Seso, France) |
Radiation | Monochromator: 2 x channel-cut double-crystal silicon [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97549 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→69.73 Å / Num. all: 52391 / Num. obs: 52391 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 48.71 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 3 / Num. unique all: 6436 / % possible all: 81.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→69.73 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.89 / SU B: 28.859 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R: 1.586 / ESU R Free: 0.327 / Stereochemistry target values: Engh & Huber / 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: 43.682 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→69.73 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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