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Yorodumi- PDB-3ntv: Crystal structure of a putative caffeoyl-CoA O-methyltransferase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ntv | ||||||
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Title | Crystal structure of a putative caffeoyl-CoA O-methyltransferase from Staphylococcus aureus | ||||||
Components | MW1564 protein | ||||||
Keywords | TRANSFERASE / rossmann fold / putative methyltransferase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å | ||||||
Authors | Qiu, W. / Lam, R. / Romanov, V. / Jones, K. / Pai, E.F. / Chirgadze, N.Y. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of a putative caffeoyl-CoA O-methyltransferase from Staphylococcus aureus Authors: Qiu, W. / Lam, R. / Romanov, V. / Jones, K. / Pai, E.F. / Chirgadze, N.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ntv.cif.gz | 105.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ntv.ent.gz | 82.3 KB | Display | PDB format |
PDBx/mmJSON format | 3ntv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ntv_validation.pdf.gz | 450.4 KB | Display | wwPDB validaton report |
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Full document | 3ntv_full_validation.pdf.gz | 454.8 KB | Display | |
Data in XML | 3ntv_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 3ntv_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/3ntv ftp://data.pdbj.org/pub/pdb/validation_reports/nt/3ntv | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27054.596 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MW2 / Gene: MW1564 / Production host: Escherichia coli (E. coli) References: UniProt: Q8NW89, UniProt: A0A0H3JWL8*PLUS, caffeoyl-CoA O-methyltransferase #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: 1.98 Å3/Da / Density % sol: 37.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 9 Details: 26% PEG4K, 0.2M lithium sulfate, 0.1M Tris-HCl, pH 9.0, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97933 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 7, 2006 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→70.46 Å / Num. all: 61267 / Num. obs: 49771 / % possible obs: 81.2 % / Redundancy: 2.84 % / Biso Wilson estimate: 21.24 Å2 / Rmerge(I) obs: 0.0593 / Rsym value: 0.0516 / Net I/σ(I): 12.36 |
Reflection shell | Resolution: 1.55→1.65 Å / Redundancy: 0.87 % / Rmerge(I) obs: 0.2449 / Mean I/σ(I) obs: 2.29 / Num. unique all: 10432 / Rsym value: 0.4328 / % possible all: 39.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.55→39.02 Å / Cor.coef. Fo:Fc: 0.9612 / Cor.coef. Fo:Fc free: 0.9484 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 27.92 Å2
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Refine analyze | Luzzati coordinate error obs: 0.177 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→39.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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