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- PDB-2j8k: Structure of the fusion of NP275 and NP276, pentapeptide repeat p... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2j8k | ||||||
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Title | Structure of the fusion of NP275 and NP276, pentapeptide repeat proteins from Nostoc punctiforme | ||||||
![]() | NP275-NP276 | ||||||
![]() | TOXIN / NOSTOC PUNCTIFORME / PENTAPEPTIDE REPEAT PROTEIN / PRP / RIGHT HANDED QUADRILATERAL BETA HELIX / RHQBH | ||||||
Function / homology | E3 ubiquitin-protein ligase SopA / Pectate Lyase C-like / 3 Solenoid / Mainly Beta![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Vetting, M.W. / Hegde, S.S. / Hazleton, K.Z. / Blanchard, J.S. | ||||||
![]() | ![]() Title: Structural Characterization of the Fusion of Two Pentapeptide Repeat Proteins, Np275 and Np276, from Nostoc Punctiforme: Resurrection of an Ancestral Protein. Authors: Vetting, M.W. / Hegde, S.S. / Hazleton, K.Z. / Blanchard, J.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.8 KB | Display | ![]() |
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PDB format | ![]() | 35.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2j8iSC 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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Unit cell |
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Components
#1: Protein | Mass: 21081.197 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: MUTATION OF STOP CODON OF NP275 TO ASN LEADS TO FUSION WITH NP276, RESIDUES 1-98 ORIGINATE FROM NP275, RESIDUES 107-181 ORIGINATE FROM NP276. INTERVENING RESIDUES ORIGINATE FROM PREVIOUSLY ...Details: MUTATION OF STOP CODON OF NP275 TO ASN LEADS TO FUSION WITH NP276, RESIDUES 1-98 ORIGINATE FROM NP275, RESIDUES 107-181 ORIGINATE FROM NP276. INTERVENING RESIDUES ORIGINATE FROM PREVIOUSLY NON-CODING DNA SEQUENCE BETWEEN NP275 AND NP276. Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MES / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Sequence details | MUTATION OF STOP CODON OF NP275 TO ASN LEADS TO FUSION WITH NP276, RESIDUES 1-98 ORIGINATE FROM ...MUTATION OF STOP CODON OF NP275 TO ASN LEADS TO FUSION WITH NP276, RESIDUES 1-98 ORIGINATE FROM NP275, RESIDUES 107-181 ORIGINATE FROM NP276. INTERVENIN |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 33.66 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 1.6 M AMMONIUM SULFATE 100 MM MES PH 6.5 PROTEIN 10 MG/ML |
-Data collection
Diffraction | Mean temperature: 194 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→15.9 Å / Num. obs: 26666 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 31.8 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 11.2 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2J8I Resolution: 1.5→59.03 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.976 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.PROTEIN IS A MONOMER IN SOLUTION
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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 mean: 13.68 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→59.03 Å
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Refine LS restraints |
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