+Open data
-Basic information
Entry | Database: PDB / ID: 4yei | ||||||
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Title | Beta1mut synthetic solenoid protein | ||||||
Components | beta1mut | ||||||
Keywords | STRUCTURAL PROTEIN / solenoid / scaffold | ||||||
Function / homology | E3 ubiquitin-protein ligase SopA / Pectate Lyase C-like / 3 Solenoid / Mainly Beta Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.55 Å | ||||||
Authors | Murray, J.W. / Kraatz, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Synthetic beta-solenoid proteins with the fragment-free computational design of a beta-hairpin extension. Authors: MacDonald, J.T. / Kabasakal, B.V. / Godding, D. / Kraatz, S. / Henderson, L. / Barber, J. / Freemont, P.S. / Murray, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yei.cif.gz | 252.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yei.ent.gz | 211.3 KB | Display | PDB format |
PDBx/mmJSON format | 4yei.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/4yei ftp://data.pdbj.org/pub/pdb/validation_reports/ye/4yei | HTTPS FTP |
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-Related structure data
Related structure data | 4yc5C 4ycqC 4ydtC 4yfoC 5di5C 5dn0C 5dnsC 5dqaC 5draC 5dzbC 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 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0 / Auth seq-ID: 20 - 234 / Label seq-ID: 20 - 234
NCS ensembles :
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-Components
#1: Protein | Mass: 24628.980 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): KRX |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 65.38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 80 mM MES pH 6.5, 128 mM magnesium sulfate. / PH range: 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 29, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 |
Reflection | Resolution: 3.55→37.43 Å / Num. all: 12716 / Num. obs: 12716 / % possible obs: 98.03 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.66 % / Rmerge(I) obs: 0.16 / Net I/av σ(I): 10.631 / Net I/σ(I): 4.8321 |
Reflection shell | Resolution: 3.55→3.65 Å / Redundancy: 4.69 % / Rmerge(I) obs: 1.03 / Mean I/σ(I) obs: 2.08 / % possible all: 97.98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.55→37.43 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.936 / SU B: 81.918 / SU ML: 0.516 / Cross valid method: THROUGHOUT / ESU R Free: 0.561 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 105.716 Å2
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Refinement step | Cycle: 1 / Resolution: 3.55→37.43 Å
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Refine LS restraints |
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