+Open data
-Basic information
Entry | Database: PDB / ID: 7vyz | ||||||
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Title | Structure of the M. tuberculosis HtrA S367A mutant | ||||||
Components | Probable serine protease HtrA1 | ||||||
Keywords | 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 / MOLECULAR REPLACEMENT / Resolution: 2.401 Å | ||||||
Authors | Gupta, A.K. / Gopal, B. | ||||||
Funding support | India, 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2023 Title: Allosteric Determinants in High Temperature Requirement A Enzymes Are Conserved and Regulate the Population of Active Conformations. Authors: Gupta, A.K. / Singh, K. / Patidar, Y. / Sharma, R. / Sardesai, A.A. / Reddy, G. / Gopal, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vyz.cif.gz | 69.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vyz.ent.gz | 48.7 KB | Display | PDB format |
PDBx/mmJSON format | 7vyz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/7vyz ftp://data.pdbj.org/pub/pdb/validation_reports/vy/7vyz | HTTPS FTP |
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-Related structure data
Related structure data | 7vz0C 7w21C 7w22C 7w23C 7w24C 7w25C 7w4rC 7w4sC 7w4tC 7w4uC 7w4vC 7w4wC 6ieoS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 32506.391 Da / Num. of mol.: 1 / Mutation: S367A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: htrA1, degP, htrA, Rv1223 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O06291, peptidase Do |
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#2: 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: 2.23 Å3/Da / Density % sol: 44.83 % |
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Crystal grow | Temperature: 298 K / Method: microbatch / 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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.401→25.54 Å / Num. obs: 10224 / % possible obs: 99.92 % / Redundancy: 3.3 % / CC1/2: 0.99 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.401→2.486 Å / Num. unique obs: 1022 / CC1/2: 0.67 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IEO Resolution: 2.401→25.54 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 2.05 / Phase error: 27.27 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.401→25.54 Å
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Refine LS restraints |
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LS refinement shell |
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