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Yorodumi- PDB-4b0t: Structure of the Pup Ligase PafA of the Prokaryotic Ubiquitin-lik... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b0t | ||||||
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Title | Structure of the Pup Ligase PafA of the Prokaryotic Ubiquitin-like Modification Pathway in Complex with ADP | ||||||
Components | PUP--PROTEIN LIGASE | ||||||
Keywords | LIGASE / PUPYLATION / DEPUPYLATION / PROKARYOTIC UBIQUITIN-LIKE PROTEIN / PROTEASOME | ||||||
Function / homology | Function and homology information prokaryotic ubiquitin-like protein ligase / protein pupylation / ligase activity, forming carbon-nitrogen bonds / ubiquitin-like protein transferase activity / proteasomal protein catabolic process / modification-dependent protein catabolic process / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | CORYNEBACTERIUM GLUTAMICUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.159 Å | ||||||
Authors | Ozcelik, D. / Barandun, J. / Schmitz, N. / Sutter, M. / Guth, E. / Damberger, F.F. / Allain, F.H.-T. / Ban, N. / Weber-Ban, E. | ||||||
Citation | Journal: Nat.Commun. / Year: 2012 Title: Structures of Pup Ligase Pafa and Depupylase Dop from the Prokaryotic Ubiquitin-Like Modification Pathway. Authors: Ozcelik, D. / Barandun, J. / Schmitz, N. / Sutter, M. / Guth, E. / Damberger, F.F. / Allain, F.H.-T. / Ban, N. / Weber-Ban, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b0t.cif.gz | 385.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b0t.ent.gz | 326.1 KB | Display | PDB format |
PDBx/mmJSON format | 4b0t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/4b0t ftp://data.pdbj.org/pub/pdb/validation_reports/b0/4b0t | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 55229.391 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CORYNEBACTERIUM GLUTAMICUM (bacteria) / Plasmid: PET EXPRESSION SYSTEM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA References: UniProt: Q8NQE1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Chemical | #3: Chemical | #4: 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: 2.73 Å3/Da / Density % sol: 55 % / Description: NONE |
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Crystal grow | pH: 9 Details: 100 MM CHES-NAOH, PH 9.0 (278 K), 200 MM LI2SO4 AND 22 % (V/V) PEG-4000 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2011 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→49 Å / Num. obs: 65412 / % possible obs: 99.2 % / Observed criterion σ(I): 2.39 / Redundancy: 3.7 % / Biso Wilson estimate: 42.71 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.15→2.2 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.39 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.159→49.417 Å / SU ML: 0.3 / σ(F): 1.35 / Phase error: 21.44 / 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 / Bsol: 50.129 Å2 / ksol: 0.329 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.159→49.417 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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