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Yorodumi- PDB-1uwv: Crystal Structure of RumA, the iron-sulfur cluster containing E. ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uwv | ||||||
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Title | Crystal Structure of RumA, the iron-sulfur cluster containing E. coli 23S Ribosomal RNA 5-Methyluridine Methyltransferase | ||||||
Components | 23S RRNA (URACIL-5-)-METHYLTRANSFERASE RUMA | ||||||
Keywords | TRANSFERASE / METHYLTRANSFERASE / RNA MODIFICATION / IRON-SULFUR CLUSTER / RNA PROCESSING | ||||||
Function / homology | Function and homology information 23S rRNA (uracil1939-C5)-methyltransferase / rRNA (uridine-C5-)-methyltransferase activity / rRNA base methylation / 4 iron, 4 sulfur cluster binding / iron ion binding / RNA binding Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å | ||||||
Authors | Lee, T.T. / Agarwalla, S. / Stroud, R.M. | ||||||
Citation | Journal: Structure / Year: 2004 Title: Crystal Structure of Ruma, an Iron-Sulfur Cluster Containing E. Coli Ribosomal RNA 5-Methyluridine Methyltransferase. Authors: Lee, T.T. / Agarwalla, S. / Stroud, R.M. #1: Journal: J.Biol.Chem. / Year: 2002 Title: Characterization of the 23 S Ribosomal RNA M5U1939 Methyltransferase from Escherichia Coli Authors: Agarwalla, S. / Kealey, J.T. / Santi, D.V. / Stroud, R.M. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uwv.cif.gz | 94 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uwv.ent.gz | 77 KB | Display | PDB format |
PDBx/mmJSON format | 1uwv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uwv_validation.pdf.gz | 395.1 KB | Display | wwPDB validaton report |
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Full document | 1uwv_full_validation.pdf.gz | 402.6 KB | Display | |
Data in XML | 1uwv_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 1uwv_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/1uwv ftp://data.pdbj.org/pub/pdb/validation_reports/uw/1uwv | 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48676.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: IRON-SULFUR CLUSTER LINKED BY CYS81, CYS87, CYS90, AND CYS162 Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P55135, Transferases; Transferring one-carbon groups; Methyltransferases |
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-Non-polymers , 5 types, 128 molecules
#2: Chemical | ChemComp-SF4 / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-PO4 / | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-Details
Compound details | CATALYZES THE FORMATION OF 5-METHYL-URIDINE AT POSITION 1939 (M-5-U1939) IN 23S RRNA. BELONGS TO ...CATALYZES THE FORMATION OF 5-METHYL-URIDINE AT POSITION 1939 (M-5-U1939) IN 23S RRNA. BELONGS TO THE RNA M5U METHYLTRAN |
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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: 2.1 Å3/Da / Density % sol: 42 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 9 Details: PROTEIN WAS CRYSTALLIZED FROM 50 MM TRIS-CL (PH 9-9.5), 10 MM NICL2, 12.5% GLYCEROL, AND 20% POLYETHYLENE GLYCOL 2000 MONOMETHYL ETHER | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 9.5 / PH range high: 9 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9786,0.9788 | |||||||||
Detector | Type: ADSC CCD QUANTUM-4 2X2 ARRAY / Detector: CCD / Date: Feb 15, 2002 / Details: MIRRORS | |||||||||
Radiation | Monochromator: DOUBLE-CRYSTAL SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.95→50 Å / Num. obs: 29176 / % possible obs: 100 % / Observed criterion σ(I): 2.6 / Redundancy: 7.5 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 18.4 | |||||||||
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.896 / Mean I/σ(I) obs: 2.6 / % possible all: 100 | |||||||||
Reflection | *PLUS Num. measured all: 632764 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.386 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. B-FACTORS ARE RESIDUAL B-FACTORS, (WHICH DO NOT INCLUDE THE CONTRIBUTION FROM THE TLS PARAMETERS). USE TLSANL (DISTRIBUTED WITH CCP4) TO ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. B-FACTORS ARE RESIDUAL B-FACTORS, (WHICH DO NOT INCLUDE THE CONTRIBUTION FROM THE TLS PARAMETERS). USE TLSANL (DISTRIBUTED WITH CCP4) TO OBTAIN THE FULL B-FACTOR.
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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 PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→50 Å
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Refine LS restraints |
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