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Yorodumi- PDB-2z9i: Crystal structure of RV0983 from Mycobacterium tuberculosis- Prot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z9i | ||||||
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Title | Crystal structure of RV0983 from Mycobacterium tuberculosis- Proteolytically active form | ||||||
Components |
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Keywords | HYDROLASE / SERINE PROTEASE / HtrA | ||||||
Function / homology | Function and homology information peptidase Do / cellular response to antibiotic / serine-type peptidase activity / protein catabolic process / serine-type endopeptidase activity / proteolysis / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Palaninathan, S.K. / Mohamedmohaideen, N.N. / Sacchettini, J.C. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Structure and function of the virulence-associated high-temperature requirement A of Mycobacterium tuberculosis Authors: Mohamedmohaideen, N.N. / Palaninathan, S.K. / Morin, P.M. / Williams, B.J. / Braunstein, M. / Tichy, S.E. / Locker, J. / Russell, D.H. / Jacobs, W.R. / Sacchettini, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z9i.cif.gz | 154.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z9i.ent.gz | 128.4 KB | Display | PDB format |
PDBx/mmJSON format | 2z9i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/2z9i ftp://data.pdbj.org/pub/pdb/validation_reports/z9/2z9i | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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-Components
#1: Protein | Mass: 32368.926 Da / Num. of mol.: 3 / Fragment: residues in database 149-464 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) References: UniProt: O53896, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Protein/peptide | Mass: 560.597 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: autolytic products / Source: (natural) Mycobacterium tuberculosis (bacteria) #3: Protein/peptide | Mass: 346.379 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: autolytic products / Source: (natural) Mycobacterium tuberculosis (bacteria) #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: 2.3 Å3/Da / Density % sol: 46.42 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 7mg/ml protein (in 50mM Tris-HCl, 1mM dithiothreitol (DTT) (pH 7.0)), 0.1M sodium acetate (pH 4.6), 0.1M cadmium chloride, 30% PEG 400 , VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.979, 0.94181, 0.97923 | ||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 30, 2004 | ||||||||||||
Radiation | Monochromator: SYNCROTRON / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.85→76.7 Å / Num. all: 76977 / Num. obs: 76977 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.12 | ||||||||||||
Reflection shell | Resolution: 1.85→1.99 Å / Redundancy: 6 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 0.87 / % possible all: 76 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.919 / SU B: 7.593 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.193 / ESU R Free: 0.181 / 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: 47.2 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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