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- PDB-5njc: E. coli Microcin-processing metalloprotease TldD/E (TldD E263A mu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5njc | ||||||||||||||||||||||||
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Title | E. coli Microcin-processing metalloprotease TldD/E (TldD E263A mutant) with hexapeptide bound | ||||||||||||||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||
![]() | Ghilarov, D. / Serebryakova, M. / Stevenson, C.E.M. / Hearnshaw, S.J. / Volkov, D. / Maxwell, A. / Lawson, D.M. / Severinov, K. | ||||||||||||||||||||||||
Funding support | ![]() ![]() ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 830.5 KB | Display | ![]() |
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PDB format | ![]() | 678.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5nj5SC ![]() 5nj9C ![]() 5njaC ![]() 5njbC ![]() 5njfC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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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: 53033.516 Da / Num. of mol.: 2 / Mutation: E263A,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.) ![]() ![]() ![]() Gene: tldD, yhdO, b3244, JW3213 / Plasmid: pCOLADuet / Production host: ![]() ![]() ![]() References: UniProt: P0AGG8, ![]() #2: Protein | Mass: 48421.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: pmbA, tldE, b4235, JW4194 / Plasmid: pCOLADuet / Production host: ![]() ![]() ![]() References: UniProt: P0AFK0, ![]() |
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-Protein/peptide , 1 types, 2 molecules EF
#3: Protein/peptide | Mass: 744.857 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Peptide adventitiously bound in the active site. From electron density a match was found to residues 49-54 of TldD, but this identification was not independently verified. Source: (gene. exp.) ![]() ![]() ![]() Production host: ![]() ![]() ![]() |
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-Non-polymers , 5 types, 2106 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.95 % |
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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: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 3, 2015 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.35→65.29 Å / Num. obs: 403735 / % possible obs: 97.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 13.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.028 / Rrim(I) all: 0.073 / Net I/σ(I): 17 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5NJ5 Resolution: 1.35→65.29 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.463 / SU ML: 0.029 / SU R Cruickshank DPI: 0.0116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.012 / ESU R Free: 0.011 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: 74.05 Å2 / Biso mean: 16.998 Å2 / Biso min: 5.39 Å2
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Refinement step | Cycle: final / Resolution: 1.35→65.29 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: 1.35→1.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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