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Yorodumi- PDB-5dlb: Crystal structure of chaperone EspG3 of ESX-3 type VII secretion ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dlb | ||||||
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Title | Crystal structure of chaperone EspG3 of ESX-3 type VII secretion system from Mycobacterium marinum M | ||||||
Components | chaperone EspG3 | ||||||
Keywords | CHAPERONE / virulence / ESX / secretion / Structural Genomics / PSI-2 / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | EspG family / EspG family / : / THIOCYANATE ION / Conserved protein Function and homology information | ||||||
Biological species | Mycobacterium marinum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77 Å | ||||||
Authors | Chan, S. / Arbing, M.A. / Kim, J. / Kahng, S. / Sawaya, M.R. / Eisenberg, D.S. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2019 Title: Structural Variability of EspG Chaperones from Mycobacterial ESX-1, ESX-3, and ESX-5 Type VII Secretion Systems. Authors: Tuukkanen, A.T. / Freire, D. / Chan, S. / Arbing, M.A. / Reed, R.W. / Evans, T.J. / Zenkeviciute, G. / Kim, J. / Kahng, S. / Sawaya, M.R. / Chaton, C.T. / Wilmanns, M. / Eisenberg, D. / ...Authors: Tuukkanen, A.T. / Freire, D. / Chan, S. / Arbing, M.A. / Reed, R.W. / Evans, T.J. / Zenkeviciute, G. / Kim, J. / Kahng, S. / Sawaya, M.R. / Chaton, C.T. / Wilmanns, M. / Eisenberg, D. / Parret, A.H.A. / Korotkov, K.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dlb.cif.gz | 123.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dlb.ent.gz | 92.7 KB | Display | PDB format |
PDBx/mmJSON format | 5dlb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dlb_validation.pdf.gz | 484 KB | Display | wwPDB validaton report |
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Full document | 5dlb_full_validation.pdf.gz | 488.7 KB | Display | |
Data in XML | 5dlb_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 5dlb_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/5dlb ftp://data.pdbj.org/pub/pdb/validation_reports/dl/5dlb | HTTPS FTP |
-Related structure data
Related structure data | 4l4wC 4rclC 5sxlC 5vbaC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Monomer according to Gel filtration |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34117.223 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium marinum (strain ATCC BAA-535 / M) (bacteria) Strain: ATCC BAA-535 / M / Gene: MMAR_0548 / Plasmid: pMAPLe4 / Details (production host): pET28 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: B2HNX0 |
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-Non-polymers , 6 types, 109 molecules
#2: Chemical | ChemComp-CXS / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-PT / #6: Chemical | ChemComp-SCN / #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 1uL 21.5mg/mL protein plus 0.5uL reservoir solution drop against 500uL reservoir solution of 1.45M ammonium sulfate, 200mM lithium sulfate, 70mM CAPS pH10.5, microseeded |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.0702 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 13, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0702 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.77→57.96 Å / Num. all: 25746 / Num. obs: 25746 / % possible obs: 89 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 37.98 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.063 / Χ2: 1.091 / Net I/σ(I): 12.6 / Num. measured all: 137146 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.77→57.96 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.2606 / WRfactor Rwork: 0.2238 / FOM work R set: 0.6999 / SU B: 9.631 / SU ML: 0.138 / SU R Cruickshank DPI: 0.1444 / SU Rfree: 0.1361 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 113.04 Å2 / Biso mean: 37.986 Å2 / Biso min: 22.15 Å2
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Refinement step | Cycle: final / Resolution: 1.77→57.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.77→1.816 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 22.6063 Å / Origin y: 43.8457 Å / Origin z: -14.0014 Å
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