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Yorodumi- PDB-2on8: Gbeta1 stabilization by in vitro evolution and computational design -
+Open data
-Basic information
Entry | Database: PDB / ID: 2on8 | ||||||
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Title | Gbeta1 stabilization by in vitro evolution and computational design | ||||||
Components | Immunoglobulin G-binding protein G | ||||||
Keywords | PROTEIN BINDING / beta sheet / alpha helix / improved hydrophobic packing of core residues | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Max, K.E.A. / Heinemann, U. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Optimization of the gbeta1 domain by computational design and by in vitro evolution: structural and energetic basis of stabilization. Authors: Wunderlich, M. / Max, K.E. / Roske, Y. / Mueller, U. / Heinemann, U. / Schmid, F.X. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). AUTHORS STATE THAT the biological unit information is unknown for this isolated domain. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2on8.cif.gz | 37.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2on8.ent.gz | 25.8 KB | Display | PDB format |
PDBx/mmJSON format | 2on8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2on8_validation.pdf.gz | 420.1 KB | Display | wwPDB validaton report |
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Full document | 2on8_full_validation.pdf.gz | 420.4 KB | Display | |
Data in XML | 2on8_validation.xml.gz | 5 KB | Display | |
Data in CIF | 2on8_validation.cif.gz | 6.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/2on8 ftp://data.pdbj.org/pub/pdb/validation_reports/on/2on8 | HTTPS FTP |
-Related structure data
Related structure data | 2onqC 1pgaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 6309.003 Da / Num. of mol.: 1 / Mutation: T1M, T2Q, Y3F, V6I, T16I, T18L, T25E, V29K, V39I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus sp. (bacteria) / Strain: G148 / Gene: spg / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19909 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.77 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 50mM Na acetate, pH 5.0, 17 mg/ml protein mixed with equal volume of 2.3M ammonium suphate, 0.1M sodium acetate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 7, 2006 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator (Si-111 crystal) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→50 Å / Num. all: 14227 / Num. obs: 13293 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.053 / Χ2: 0.789 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.34→1.39 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.365 / Num. unique all: 770 / Rsym value: 0.365 / Χ2: 0.737 / % possible all: 56.4 |
-Phasing
Phasing MR | Rfactor: 0.377 / Cor.coef. Fo:Fc: 0.514 / Cor.coef. Io to Ic: 0.161
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PGA Resolution: 1.35→19 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.927 / SU ML: 0.035 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.058 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE STRUCTURE FACTORS ARE TWINNED. TWIN TYPE: PARTIAL MEROHEDRAL TWIN TWIN FRACTION: 0.235 TWINNING RELATIONSHIP RELATES REFLECTIONS WITH ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE STRUCTURE FACTORS ARE TWINNED. TWIN TYPE: PARTIAL MEROHEDRAL TWIN TWIN FRACTION: 0.235 TWINNING RELATIONSHIP RELATES REFLECTIONS WITH INDICES h,k,l to h,k,-l. Authors also state that the structure was refined using a combination of isotropic (atomic) and TLS refinement. The whole molecule was defined as one TLS group. The atomic B-values are reported as anisotropic B-values which were calculated by combining the isotropic B-values and TLS parameters using TLSANL program from the CCP4 suite.
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.64 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.397 Å / Total num. of bins used: 15
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