+Open data
-Basic information
Entry | Database: PDB / ID: 2fsx | ||||||
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Title | Crystal structure of Rv0390 from M. tuberculosis | ||||||
Components | COG0607: Rhodanese-related sulfurtransferase | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Rv0390 Br SAD data with Fbar / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | Function and homology information Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Bursey, E.H. / Radhakannan, T. / Yu, M. / Segelke, B.W. / Lekin, T. / Toppani, D. / Chang, Y.-B. / Kaviratne, T. / Woodruff, T. / Terwilliger, T.C. ...Bursey, E.H. / Radhakannan, T. / Yu, M. / Segelke, B.W. / Lekin, T. / Toppani, D. / Chang, Y.-B. / Kaviratne, T. / Woodruff, T. / Terwilliger, T.C. / Hung, L.-W. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Rv0390 from Mycobacterium tuberculosis Authors: Bursey, E.H. / Radhakannan, T. / Yu, M. / Segelke, B.W. / Lekin, T. / Toppani, D. / Chang, Y.-B. / Kaviratne, T. / Woodruff, T. / Terwilliger, T.C. / Hung, L.-W. | ||||||
History |
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Remark 999 | SEQUENCE THE PROTEIN USED TO SOLVE THIS STRUCTURE WAS OBTAINED FROM A DIFFERENT STRAIN H37Rv OF THE ...SEQUENCE THE PROTEIN USED TO SOLVE THIS STRUCTURE WAS OBTAINED FROM A DIFFERENT STRAIN H37Rv OF THE SAME ORGANISM |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fsx.cif.gz | 43.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fsx.ent.gz | 30 KB | Display | PDB format |
PDBx/mmJSON format | 2fsx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fsx_validation.pdf.gz | 433.2 KB | Display | wwPDB validaton report |
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Full document | 2fsx_full_validation.pdf.gz | 434 KB | Display | |
Data in XML | 2fsx_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 2fsx_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/2fsx ftp://data.pdbj.org/pub/pdb/validation_reports/fs/2fsx | HTTPS FTP |
-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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Unit cell |
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Details | It appeared to be a monomer judged by the crystal structure |
-Components
#1: Protein | Mass: 16449.113 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: F11 / Gene: Rv0390 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 76785673, UniProt: P95198*PLUS | ||||
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#2: Chemical | ChemComp-BR / #3: Chemical | ChemComp-SO4 / | #4: 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: 50.81 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Sodium Citrate 1.0176M, MES 0.1M, Ammonium Sulfate 0.31752M , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.92 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2005 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 15254 / Num. obs: 15238 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 5 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.5 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→30.4 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.248 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.113 / 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: 12.596 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 7.079 Å / Origin y: 10.435 Å / Origin z: 43.991 Å
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Refinement TLS group |
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