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Yorodumi- PDB-3knq: Beta Turn Optimization of the Gene-3-Protein of Filamentous Phage Fd -
+Open data
-Basic information
Entry | Database: PDB / ID: 3knq | ||||||
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Title | Beta Turn Optimization of the Gene-3-Protein of Filamentous Phage Fd | ||||||
Components | Attachment protein G3P | ||||||
Keywords | VIRAL PROTEIN / filamentous phage / beta turn / rational design / protein stabilization / protein engineering / protein folding / Disulfide bond / Phage recognition / Transmembrane | ||||||
Function / homology | Function and homology information viral extrusion / virion attachment to host cell pilus / adhesion receptor-mediated virion attachment to host cell / host cell membrane / viral capsid / entry receptor-mediated virion attachment to host cell / membrane Similarity search - Function | ||||||
Biological species | Enterobacteria phage fd (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å | ||||||
Authors | Jakob, R.P. / Dobbek, H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Elimination of a cis-proline-containing loop and turn optimization stabilizes a protein and accelerates its folding. Authors: Jakob, R.P. / Zierer, B.K. / Weininger, U. / Hofmann, S.D. / Lorenz, S.H. / Balbach, J. / Dobbek, H. / Schmid, F.X. | ||||||
History |
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Remark 999 | AUTHOR STATES THAT RESIDUES 157-162(GLN GLY THR ASP PRO VAL) OF UNP ENTRY P03661 WAS DELETED AND ...AUTHOR STATES THAT RESIDUES 157-162(GLN GLY THR ASP PRO VAL) OF UNP ENTRY P03661 WAS DELETED AND REPLACED BY RESIDUES 157-159 (VAL ASN GLY) IN THE CRYSTALLIZED PROTEIN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3knq.cif.gz | 166.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3knq.ent.gz | 132.2 KB | Display | PDB format |
PDBx/mmJSON format | 3knq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3knq_validation.pdf.gz | 447.9 KB | Display | wwPDB validaton report |
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Full document | 3knq_full_validation.pdf.gz | 453.4 KB | Display | |
Data in XML | 3knq_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 3knq_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/3knq ftp://data.pdbj.org/pub/pdb/validation_reports/kn/3knq | HTTPS FTP |
-Related structure data
Related structure data | 3dgsS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24317.510 Da / Num. of mol.: 2 / Fragment: Gene-3-Protein, residue 19-238 Mutation: C7S, P11S, T13I, N15G, R29W, C36I, N39K, C46I, C53V, G55A, T56I, I60V, T101I, Q129H, N138G, R144V, Q145N, A147V, C188V, F199L, C201A, S207L, D209Y, Replacment of LoopQ157-V162 with the sequence VNG Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage fd (virus) / Gene: 3, III / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P03661 #2: 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: 2.43 Å3/Da / Density % sol: 49.44 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 15-20% PEG3350, 0.2M NH4Cl, 0.05 M CaCl2, 0.1 M Tris/Cl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.13→33.77 Å / Num. obs: 26294 / % possible obs: 96.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 13.4 / Biso Wilson estimate: 35.88 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.13→2.19 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 47 / Num. unique all: 1532 / Rsym value: 0.02 / % possible all: 76.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3dgs.PDB Resolution: 2.13→33.77 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 54.37 Å2
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Refine analyze | Luzzati coordinate error obs: 0.37 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13→33.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.13→2.19 Å / Total num. of bins used: 13
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