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Yorodumi- PDB-2uyo: Crystal structure of ML2640c from Mycobacterium leprae in an hexa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2uyo | ||||||
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Title | Crystal structure of ML2640c from Mycobacterium leprae in an hexagonal crystal form | ||||||
Components | HYPOTHETICAL PROTEIN ML2640 | ||||||
Keywords | TRANSFERASE / HYPOTHETICAL PROTEIN / PUTATIVE METHYLTRANSFERASE | ||||||
Function / homology | Function and homology information Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM LEPRAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Grana, M. / Buschiazzo, A. / Wehenkel, A. / Haouz, A. / Miras, I. / Shepard, W. / Alzari, P.M. | ||||||
Citation | Journal: Protein Sci. / Year: 2007 Title: The Crystal Structure of M. Leprae Ml2640C Defines a Large Family of Putative S-Adenosylmethionine- Dependent Methyltransferases in Mycobacteria. Authors: Grana, M. / Haouz, A. / Buschiazzo, A. / Miras, I. / Wehenkel, A. / Bondet, V. / Shepard, W. / Schaeffer, F. / Cole, S.T. / Alzari, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2uyo.cif.gz | 70.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uyo.ent.gz | 50.6 KB | Display | PDB format |
PDBx/mmJSON format | 2uyo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2uyo_validation.pdf.gz | 416.7 KB | Display | wwPDB validaton report |
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Full document | 2uyo_full_validation.pdf.gz | 420.7 KB | Display | |
Data in XML | 2uyo_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 2uyo_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/2uyo ftp://data.pdbj.org/pub/pdb/validation_reports/uy/2uyo | HTTPS FTP |
-Related structure data
Related structure data | 2ckdSC 2uyqC 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
#1: Protein | Mass: 34492.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM LEPRAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9CCZ4 |
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#2: 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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | pH: 9 / Details: 0.8 M SODIUM CITRATE, 100 MM BICINE, PH 9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 7, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9756 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 37485 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.6 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CKD Resolution: 1.7→65.51 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.203 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.102 / 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: 28.72 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→65.51 Å
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Refine LS restraints |
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