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Yorodumi- PDB-3hss: A higher resolution structure of Rv0554 from Mycobacterium tuberc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hss | ||||||
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Title | A higher resolution structure of Rv0554 from Mycobacterium tuberculosis complexed with malonic acid | ||||||
Components | putative BromoperoxidaseBromide peroxidase | ||||||
Keywords | HYDROLASE / alpha beta hydrolase / Oxidoreductase / Peroxidase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Johnston, J.M. / Baker, E.N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2010 Title: Structural and functional analysis of Rv0554 from Mycobacterium tuberculosis: testing a putative role in menaquinone biosynthesis. Authors: Johnston, J.M. / Jiang, M. / Guo, Z. / 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 | 3hss.cif.gz | 131.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hss.ent.gz | 100.2 KB | Display | PDB format |
PDBx/mmJSON format | 3hss.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hs/3hss ftp://data.pdbj.org/pub/pdb/validation_reports/hs/3hss | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The protein is mostly a dimer in solution and PISA predicts a dimer is likely in the crystal too. This dimer is consistent with the one seen in the related entry structure. |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 32254.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: bpoC, MT0580, Rv0554 / Production host: Escherichia coli (E. coli) References: UniProt: O06420, UniProt: P9WNH1*PLUS, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases |
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-Non-polymers , 6 types, 529 molecules
#2: Chemical | ChemComp-TRS / | ||||||||
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#3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-ACT / | #7: 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: 2.64 Å3/Da / Density % sol: 53.46 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.92 Details: 95% ( 0.1M NaAcetate pH 4.92, 2% MDP, 15% ethylene glycol) with 5% 1.65M Malonic Acid Protein had PEP added to it as well. , VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95665 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95665 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 54772 / % possible obs: 99 % / Redundancy: 29.1 % / Rmerge(I) obs: 0.087 / Χ2: 1.024 / Net I/σ(I): 52.964 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 25.9 % / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 6.1 / Num. unique all: 5318 / Χ2: 0.758 / % possible all: 98.2 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→40.32 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.214 / WRfactor Rwork: 0.186 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.863 / SU R Cruickshank DPI: 0.14 / SU Rfree: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.8 Å2 / Biso mean: 25.169 Å2 / Biso min: 9.5 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→40.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.897→1.947 Å / Total num. of bins used: 20
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