+Open data
-Basic information
Entry | Database: PDB / ID: 4fak | ||||||
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Title | Crystal Structure of OrfX in Complex with S-Adenosylmethionine | ||||||
Components | Ribosomal RNA large subunit methyltransferase H | ||||||
Keywords | TRANSFERASE / RIBOSOMAL PROTEIN / alpha/beta methyltransferase Rossmann fold / rRNA methylation / AdoMet / rRNA | ||||||
Function / homology | Function and homology information 23S rRNA (pseudouridine1915-N3)-methyltransferase / rRNA (pseudouridine-N3-)-methyltransferase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Safo, M.K. / Musayev, F.N. / Boundy, S. / Archer, G.L. / Rife, J.P. / O'Farrell, H.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Characterization of the Staphylococcus aureus rRNA Methyltransferase Encoded by orfX, the Gene Containing the Staphylococcal Chromosome Cassette mec (SCCmec) Insertion Site. Authors: Boundy, S. / Safo, M.K. / Wang, L. / Musayev, F.N. / O'Farrell, H.C. / Rife, J.P. / Archer, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fak.cif.gz | 53.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fak.ent.gz | 36.2 KB | Display | PDB format |
PDBx/mmJSON format | 4fak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fak_validation.pdf.gz | 794.4 KB | Display | wwPDB validaton report |
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Full document | 4fak_full_validation.pdf.gz | 797.7 KB | Display | |
Data in XML | 4fak_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 4fak_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/4fak ftp://data.pdbj.org/pub/pdb/validation_reports/fa/4fak | HTTPS FTP |
-Related structure data
Related structure data | 1vh0S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 18752.818 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: RN450M / Gene: orfx, rlmH / Plasmid: pET30a / Production host: Escherichia coli (E. coli) References: UniProt: P0C1V0, 23S rRNA (pseudouridine1915-N3)-methyltransferase |
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#2: Chemical | ChemComp-SAM / |
#3: Chemical | ChemComp-PG4 / |
#4: Chemical | ChemComp-PO4 / |
#5: 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: 2.44 Å3/Da / Density % sol: 49.51 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20% PEG 550 MME, 5 mM ZnSO4, 0.1M Na 2-(N-morpholino) ethanesulfonate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 1, 2010 / Details: mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→28.6 Å / Num. all: 19664 / Num. obs: 20528 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 5.4 / Num. unique all: 1862 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VH0 Resolution: 1.7→26.43 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1372577.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.9051 Å2 / ksol: 0.355692 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→26.43 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.76 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 10
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