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Yorodumi- PDB-2ymv: Structure of Reduced M Smegmatis 5246, a homologue of M.Tuberculo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ymv | ||||||
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Title | Structure of Reduced M Smegmatis 5246, a homologue of M.Tuberculosis Acg | ||||||
Components | ACG NITROREDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / DORMANCY / REDUCED FMN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | MYCOBACTERIUM SMEGMATIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Chauviac, F.-X. / Bommer, M. / Dobbek, H. / Keep, N.H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Crystal Structure of Reduced Msacg, a Putative Nitroreductase from Mycobacterium Smegmatis and a Close Homologue of Mycobacterium Tuberculosis Acg. Authors: Chauviac, F.-X. / Bommer, M. / Yan, J. / Parkin, G. / Daviter, T. / Lowden, P. / Raven, E.L. / Thalassinos, K. / Keep, N.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ymv.cif.gz | 168 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ymv.ent.gz | 140.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ymv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/2ymv ftp://data.pdbj.org/pub/pdb/validation_reports/ym/2ymv | HTTPS FTP |
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-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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36587.418 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC2-155 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: A0R2V4 |
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-Non-polymers , 6 types, 527 molecules
#2: Chemical | ChemComp-FNR / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-IMD / | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | FMN IS THE ONLY BIOLOGICAL RELAVENT HETROGEN IN THIS ENTRY. ALL OTHER HETATOMS ARE COMPONENTS OF ...FMN IS THE ONLY BIOLOGICAL |
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Sequence details | EXTRA SER ON THE N-TERMINUS FROM TEV CLEAVAGE SITE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.82 Å3/Da / Density % sol: 74.1 % Description: STRUCTURE ORIGINALY SOLVED USING AUTO-RICKSHAW AND 2.4 A DATASET. |
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Crystal grow | pH: 6.5 Details: 0.1M IMIDAZOLE/MES PH 6.5, 30%(V/V)PEG550MME, 25 MM NA FORMATE, 25 MM AM ACETATE, 25 MM NA CITRATE, 25 MM NAK TARTRATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9148 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 28, 2012 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9148 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→26.57 Å / Num. obs: 92796 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 15.35 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SAD MODEL AT 2.4 A FROM ANOTHER DATASET Resolution: 1.6→26.568 Å / SU ML: 0.12 / σ(F): 1.34 / Phase error: 12.95 / Stereochemistry target values: ML Details: RESIDUES 1-2 AND 330 DISORDERED LOOP 292-294 IN MULTIPLE CONFORMATIONS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→26.568 Å
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Refine LS restraints |
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LS refinement shell |
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