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Yorodumi- PDB-3lt3: Crystal structure of Rv3671c from M. tuberculosis H37Rv, Ser343Al... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lt3 | ||||||
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Title | Crystal structure of Rv3671c from M. tuberculosis H37Rv, Ser343Ala mutant, inactive form | ||||||
Components | POSSIBLE MEMBRANE-ASSOCIATED SERINE PROTEASE | ||||||
Keywords | HYDROLASE / serine protease / H37Rv / HtrA / protease | ||||||
Function / homology | Function and homology information toxin biosynthetic process / evasion of host immune response / response to acidic pH / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / peptidoglycan-based cell wall / membrane => GO:0016020 / serine-type endopeptidase activity / proteolysis / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Biswas, T. / Small, J. / Vandal, O. / Ehrt, S. / Tsodikov, O.V. | ||||||
Citation | Journal: Structure / Year: 2010 Title: Structural insight into serine protease Rv3671c that Protects M. tuberculosis from oxidative and acidic stress. Authors: Biswas, T. / Small, J. / Vandal, O. / Odaira, T. / Deng, H. / Ehrt, S. / Tsodikov, O.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lt3.cif.gz | 156.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lt3.ent.gz | 123.7 KB | Display | PDB format |
PDBx/mmJSON format | 3lt3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/3lt3 ftp://data.pdbj.org/pub/pdb/validation_reports/lt/3lt3 | HTTPS FTP |
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-Related structure data
Related structure data | 3k6yC 3k6zSC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 22071.947 Da / Num. of mol.: 2 / Fragment: Rv3671c (179-397) / Mutation: S343A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: MT3772, Rv3671c / Plasmid: pET19b-pps / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O69639, UniProt: P9WHR9*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: 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: 2.13 Å3/Da / Density % sol: 42.17 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M Tris-HCl, 2.1 M ammonium phosphate monobasic, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.002 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 15, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.002 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 19845 / Num. obs: 18853 / % possible obs: 95 % / Observed criterion σ(I): 3.8 / Redundancy: 2.1 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 2.1→2.14 Å / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 3.8 / % possible all: 84.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3K6Z Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.888 / SU B: 15.469 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 34.377 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.157 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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