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Yorodumi- PDB-7caq: Versatile cis-prenyltransferase MM_0014 from Methanosarcina mazei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7caq | |||||||||
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Title | Versatile cis-prenyltransferase MM_0014 from Methanosarcina mazei (crystal type: substrate-free) | |||||||||
Components | cis-prenyltransferase MM_0014 | |||||||||
Keywords | TRANSFERASE / cis-prenyltransferase / Methanosarcina mazei / archaea. isoprenoid | |||||||||
Function / homology | PALMITIC ACID / PHOSPHATE ION Function and homology information | |||||||||
Biological species | Methanosarcina mazei Go1 (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | |||||||||
Authors | Unno, H. / Hemmi, H. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2021 Title: A versatile cis-prenyltransferase from Methanosarcina mazei catalyzes both C- and O-prenylations. Authors: Okada, M. / Unno, H. / Emi, K.I. / Matsumoto, M. / Hemmi, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7caq.cif.gz | 105.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7caq.ent.gz | 78.9 KB | Display | PDB format |
PDBx/mmJSON format | 7caq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7caq_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7caq_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7caq_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 7caq_validation.cif.gz | 30 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/7caq ftp://data.pdbj.org/pub/pdb/validation_reports/ca/7caq | HTTPS FTP |
-Related structure data
Related structure data | 7carC 7casC 7cavC 7cc3C 1x07S S: Starting model for refinement 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: 25688.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina mazei Go1 (archaea) / Gene: MM_0014 / Production host: Escherichia coli (E. coli) #2: Chemical | #3: Chemical | ChemComp-PLM / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | Sequence details | THE GENEBANK ACCESSION NUMBER IS 24771896 FOR THE PROTEIN. | |
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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: 2.55 Å3/Da / Density % sol: 51.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 4 mM cobalt (II) chloride, 4 mM nickel (II) chloride, 4 mM cadmium chloride, 4 mM magnesium chloride, 0.075 M HEPES, pH7.5, 9% PEG 3350, 25% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→65.3 Å / Num. obs: 59466 / % possible obs: 99.7 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.69→1.78 Å / Rmerge(I) obs: 0.816 / Mean I/σ(I) obs: 3 / Num. unique obs: 8623 / CC1/2: 0.846 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1X07 Resolution: 1.69→40.04 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.794 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.109 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.915 Å2
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Refinement step | Cycle: 1 / Resolution: 1.69→40.04 Å
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