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Yorodumi- PDB-6ieo: Crystal structure of Mycobacterium tuberculosis HtrA1 (Rv1223) in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ieo | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis HtrA1 (Rv1223) in regulated conformation | ||||||
Components | Probable serine protease HtrA (DEGP protein) | ||||||
Keywords | MEMBRANE PROTEIN / Hydrolase / HtrA family of serine protease / chymotrypsin like / Periplasm / Protein quality control and signal transduction | ||||||
Function / homology | Function and homology information peptidase Do / peptidoglycan-based cell wall / serine-type endopeptidase activity / proteolysis / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Gupta, A.K. / Gopal, B. | ||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2018 Title: The crystal structure of Mycobacterium tuberculosis high-temperature requirement A protein reveals an autoregulatory mechanism. Authors: Gupta, A.K. / Behera, D. / Gopal, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ieo.cif.gz | 72.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ieo.ent.gz | 50.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ieo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/6ieo ftp://data.pdbj.org/pub/pdb/validation_reports/ie/6ieo | HTTPS FTP |
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-Related structure data
Related structure data | 1y8tS S: Starting model for refinement |
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Similar structure data |
-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
#1: Protein | Mass: 32522.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: htrA, Rv1223 / Production host: Escherichia coli (E. coli) / References: UniProt: O06291 |
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#2: Chemical | ChemComp-PMS / |
#3: 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: 2.22 Å3/Da / Density % sol: 44.52 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.1M HEPES, 1.4M Sodium Citrate tribasic dihydrate pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 28, 2018 / Details: CRL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→37.04 Å / Num. obs: 23356 / % possible obs: 99.69 % / Redundancy: 4.6 % / Biso Wilson estimate: 29.05 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.071 / Rrim(I) all: 0.115 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.82→1.89 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2197 / CC1/2: 0.517 / Rpim(I) all: 0.729 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Y8T Resolution: 1.83→37.04 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.861 / SU ML: 0.138 / Cross valid method: FREE R-VALUE / ESU R: 0.141 / ESU R Free: 0.134 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34 Å2
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Refinement step | Cycle: 1 / Resolution: 1.83→37.04 Å
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Refine LS restraints |
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