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Yorodumi- PDB-5nja: E. coli Microcin-processing metalloprotease TldD/E with angiotens... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nja | ||||||||||||||||||||||||
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Title | E. coli Microcin-processing metalloprotease TldD/E with angiotensin analogue bound | ||||||||||||||||||||||||
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Keywords | HYDROLASE / metalloprotease / microcin / CcdA / DNA gyrase | ||||||||||||||||||||||||
Function / homology | Function and homology information peptidase complex / regulation of blood volume by renin-angiotensin / response to muscle activity involved in regulation of muscle adaptation / regulation of renal sodium excretion / : / type 2 angiotensin receptor binding / maintenance of blood vessel diameter homeostasis by renin-angiotensin / negative regulation of neurotrophin TRK receptor signaling pathway / regulation of extracellular matrix assembly / positive regulation of activation of Janus kinase activity ...peptidase complex / regulation of blood volume by renin-angiotensin / response to muscle activity involved in regulation of muscle adaptation / regulation of renal sodium excretion / : / type 2 angiotensin receptor binding / maintenance of blood vessel diameter homeostasis by renin-angiotensin / negative regulation of neurotrophin TRK receptor signaling pathway / regulation of extracellular matrix assembly / positive regulation of activation of Janus kinase activity / regulation of renal output by angiotensin / positive regulation of NAD(P)H oxidase activity / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / renin-angiotensin regulation of aldosterone production / renal system process / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of extracellular matrix assembly / positive regulation of CoA-transferase activity / positive regulation of macrophage derived foam cell differentiation / low-density lipoprotein particle remodeling / vasoconstriction / type 1 angiotensin receptor binding / response to angiotensin / positive regulation of extrinsic apoptotic signaling pathway / Hydrolases; Acting on peptide bonds (peptidases) / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of cardiac muscle hypertrophy / positive regulation of gap junction assembly / regulation of vasoconstriction / regulation of cardiac conduction / positive regulation of epithelial to mesenchymal transition / blood vessel remodeling / positive regulation of protein tyrosine kinase activity / Metabolism of Angiotensinogen to Angiotensins / nitric oxide mediated signal transduction / positive regulation of protein metabolic process / Peptide ligand-binding receptors / negative regulation of MAP kinase activity / positive regulation of endothelial cell migration / kidney development / regulation of cell growth / positive regulation of cytokine production / angiotensin-activated signaling pathway / growth factor activity / serine-type endopeptidase inhibitor activity / hormone activity / PPARA activates gene expression / protein processing / regulation of blood pressure / positive regulation of inflammatory response / positive regulation of miRNA transcription / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / positive regulation of fibroblast proliferation / cell-cell signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / regulation of cell population proliferation / G alpha (i) signalling events / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / regulation of apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / iron ion binding / G protein-coupled receptor signaling pathway / positive regulation of DNA-templated transcription / extracellular space / extracellular exosome / zinc ion binding / extracellular region / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||||||||
Biological species | Escherichia coli str. K-12 substr. MG1655 (bacteria) Homo sapiens (human) | ||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å | ||||||||||||||||||||||||
Authors | Ghilarov, D. / Serebryakova, M. / Stevenson, C.E.M. / Hearnshaw, S.J. / Volkov, D. / Maxwell, A. / Lawson, D.M. / Severinov, K. | ||||||||||||||||||||||||
Funding support | Russian Federation, Poland, United Kingdom, 7items
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Citation | Journal: Structure / Year: 2017 Title: The Origins of Specificity in the Microcin-Processing Protease TldD/E. Authors: Ghilarov, D. / Serebryakova, M. / Stevenson, C.E.M. / Hearnshaw, S.J. / Volkov, D.S. / Maxwell, A. / Lawson, D.M. / Severinov, K. | ||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nja.cif.gz | 832.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nja.ent.gz | 678.4 KB | Display | PDB format |
PDBx/mmJSON format | 5nja.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/5nja ftp://data.pdbj.org/pub/pdb/validation_reports/nj/5nja | HTTPS FTP |
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-Related structure data
Related structure data | 5nj5SC 5nj9C 5njbC 5njcC 5njfC S: Starting model for refinement C: citing same article (ref.) |
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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: Component-ID: 0 / Refine code: 0
NCS ensembles :
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-Components
-Metalloprotease ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 53091.551 Da / Num. of mol.: 2 / Mutation: G401D Source method: isolated from a genetically manipulated source Details: The TldD protein was expressed with a fourteen residue nickel affinity tag with sequence MGSSHHHHHHSQDP appended to the N-terminus of the full-length amino acid sequence Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria) Gene: tldD, yhdO, b3244, JW3213 / Plasmid: pCOLADuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): star References: UniProt: P0AGG8, Hydrolases; Acting on peptide bonds (peptidases) #2: Protein | Mass: 48421.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria) Gene: pmbA, tldE, b4235, JW4194 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): star References: UniProt: P0AFK0, Hydrolases; Acting on peptide bonds (peptidases) |
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-Protein/peptide , 1 types, 2 molecules EF
#3: Protein/peptide | Mass: 400.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Angiotensin-derived peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P01019*PLUS |
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-Non-polymers , 5 types, 2113 molecules
#4: Chemical | #5: Chemical | ChemComp-MES / #6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-NA / #8: 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: 2.29 Å3/Da / Density % sol: 46.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: NULL |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 19, 2015 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.4→86.76 Å / Num. obs: 349069 / % possible obs: 97.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 12.1 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.048 / Rrim(I) all: 0.124 / Net I/σ(I): 9.6 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5NJ5 Resolution: 1.4→86.76 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.357 / SU ML: 0.026 / SU R Cruickshank DPI: 0.0123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.012 / ESU R Free: 0.012 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 59.78 Å2 / Biso mean: 16.345 Å2 / Biso min: 7.46 Å2
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Refinement step | Cycle: final / Resolution: 1.4→86.76 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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