+Open data
-Basic information
Entry | Database: PDB / ID: 1nxj | ||||||
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Title | Structure of Rv3853 from Mycobacterium tuberculosis | ||||||
Components | Probable S-adenosylmethionine:2-demethylmenaquinone methyltransferase | ||||||
Keywords | UNKNOWN FUNCTION / beta/beta/alpha domain / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | Function and homology information 4-hydroxy-4-methyl-2-oxoglutarate aldolase / 4-hydroxy-4-methyl-2-oxoglutarate aldolase activity / oxaloacetate decarboxylase / ribonuclease inhibitor activity / regulation of RNA metabolic process / oxaloacetate decarboxylase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.9 Å | ||||||
Authors | Johnston, J.M. / Arcus, V.L. / Baker, E.N. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: J.Bacteriol. / Year: 2003 Title: Crystal Structure of a Putative Methyltransferase from Mycobacterium tuberculosis: Misannotation of a Genome Clarified by Protein Structural Analysis Authors: Johnston, J.M. / Arcus, V.L. / Morton, C.J. / Parker, M.W. / Baker, E.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nxj.cif.gz | 103.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nxj.ent.gz | 79 KB | Display | PDB format |
PDBx/mmJSON format | 1nxj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/1nxj ftp://data.pdbj.org/pub/pdb/validation_reports/nx/1nxj | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | The biological assembly is a trimer. Trimers can be generated from each of the three monomers in the assymmetric unit by the operations: -y, x-y, z; y-x, -x, z; -x, -y, z+1/2; y, y-x, z+1/2 and x-y, x, z+1/2 |
-Components
#1: Protein | Mass: 19380.758 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MENG / Plasmid: pProEX Hta / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pRI592 References: UniProt: P0A666, UniProt: P9WGY3*PLUS, Transferases; Transferring one-carbon groups #2: Chemical | #3: Chemical | #4: 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: 3.43 Å3/Da / Density % sol: 63.88 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.45M sodium potassium tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | |||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 63.9 % | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8452 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 20, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8452 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. all: 54630 / Num. obs: 54241 / % possible obs: 99.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 9.4 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 3.1 / Num. unique all: 5249 / % possible all: 96.1 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 54630 / Redundancy: 3.35 % |
Reflection shell | *PLUS % possible obs: 96.1 % |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.9→24.61 Å / Rfactor Rfree error: 0.003 / 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: 48.1134 Å2 / ksol: 0.395904 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→24.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.22 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Num. reflection Rwork: 5344 |