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Yorodumi- PDB-7vep: Crystal structure and biophysical characterization of TPR domain ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vep | ||||||
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Title | Crystal structure and biophysical characterization of TPR domain of EccA5 from ESX-5 pathway of Mycobacterium tuberculosis H37RVR | ||||||
Components | ESX-5 secretion system protein EccA5 | ||||||
Keywords | HYDROLASE / EccA5 / AAA+ATPase / TPR domain | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å | ||||||
Authors | Ramachandran, R. / Sharma, V.K. / Vishwakarma, J. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published Title: Crystal structure and biophysical characterization of TPR domain of EccA5 from ESX-5 pathway of Mycobacterium tuberculosis H37RVR Authors: Ramachandran, R. / Sharma, V.K. / Vishwakarma, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vep.cif.gz | 70.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vep.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 7vep.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/7vep ftp://data.pdbj.org/pub/pdb/validation_reports/ve/7vep | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30931.049 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: eccA5, Rv1798, MTV049.20 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P9WPI1 | ||||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.02 % / Description: 3D rod shaped crystals |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: Lithium sulfate, sodium citrate 5.6, Ammonium sulfate, glycerol as additive |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→43.14 Å / Num. obs: 20585 / % possible obs: 99.2 % / Redundancy: 5.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.067 / Rrim(I) all: 0.116 / Χ2: 1.03 / Net I/av σ(I): 13.4 / Net I/σ(I): 2.3 |
Reflection shell | Resolution: 2.15→2.2 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.631 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1717 / CC1/2: 0.715 / Rpim(I) all: 0.474 / Rrim(I) all: 0.793 / Χ2: 1.02 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.15→39.319 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.57 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.35 Å2 / Biso mean: 34.0412 Å2 / Biso min: 15.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.15→39.319 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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