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Yorodumi- PDB-3fil: Structural and energetic determinants for hyperstable variants of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fil | ||||||
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Title | Structural and energetic determinants for hyperstable variants of GB1 obtained from in-vitro evolution | ||||||
Components | (Immunoglobulin G-binding protein G) x 2 | ||||||
Keywords | PROTEIN BINDING / dimerization / beta sheet / alpha helix / improved hydrophobic packing of core residues / Cell wall / IgG-binding protein / Peptidoglycan-anchor / Secreted | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus sp. 'group G' (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.88 Å | ||||||
Authors | Max, K.E.A. / Heinemann, U. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Dimer Formation of a Stabilized Gbeta1 Variant: A Structural and Energetic Analysis Authors: Thoms, S. / Max, K.E.A. / Wunderlich, M. / Jacso, T. / Lilie, H. / Reif, B. / Heinemann, U. / Schmid, F.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fil.cif.gz | 70.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fil.ent.gz | 52.1 KB | Display | PDB format |
PDBx/mmJSON format | 3fil.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fil_validation.pdf.gz | 416.3 KB | Display | wwPDB validaton report |
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Full document | 3fil_full_validation.pdf.gz | 416.6 KB | Display | |
Data in XML | 3fil_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 3fil_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/3fil ftp://data.pdbj.org/pub/pdb/validation_reports/fi/3fil | HTTPS FTP |
-Related structure data
Related structure data | 1pgaS 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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Unit cell |
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-Components
#1: Antibody | Mass: 6249.999 Da / Num. of mol.: 1 Fragment: immunoglobulin binding domain, UNP residues 303-357 Mutation: T2Q, E15V, T16L, T18I, N37L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus sp. 'group G' (bacteria) / Strain: G148 / Gene: spg / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(de3) / References: UniProt: P19909 |
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#2: Antibody | Mass: 6221.989 Da / Num. of mol.: 1 Fragment: immunoglobulin binding domain, UNP residues 303-357 Mutation: T2Q, E15V, T16L, T18I, N37L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus sp. 'group G' (bacteria) / Strain: G148 / Gene: spg / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(de3) / References: UniProt: P19909 |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Sequence details | FME IS INITIATING N-FORMYLMETHIONINE THAT IS THE BIOLOGICAL STARTING RESIDUE IN E. COLI WHICH HAS ...FME IS INITIATING |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 39.4 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: protein solution: 50mM sodium acetate pH 5.6, 50mg/ml protein. reservoir solution: 25% PEG 3350, 0.1M citric acids pH 3.5. Drop 400nl protein solution & 400nl reservoir solution, 80 micro-l ...Details: protein solution: 50mM sodium acetate pH 5.6, 50mg/ml protein. reservoir solution: 25% PEG 3350, 0.1M citric acids pH 3.5. Drop 400nl protein solution & 400nl reservoir solution, 80 micro-l reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.88561 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Mar 6, 2006 Details: Mirror 1: Silicon, active surface 50nm Rh-coated. Mirror 2: Glas, active surface 50 nm Rh-coated. |
Radiation | Monochromator: silicon-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.88561 Å / Relative weight: 1 |
Reflection | Resolution: 0.842→19.466 Å / Num. all: 87156 / Num. obs: 86548 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Redundancy: 7.08 % / Biso Wilson estimate: 11.564 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.063 / Net I/σ(I): 13.26 |
Reflection shell | Resolution: 0.84→0.98 Å / Redundancy: 5.82 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.56 / Num. unique all: 9687 / Rsym value: 0.775 / % possible all: 84.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PGA Resolution: 0.88→19.466 Å / Num. parameters: 10668 / Num. restraintsaints: 13229 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: According to PROCHECK and WHATCHECK, no backbone outliers were reported. The ASN A8 backbone and sidechain groups are centered in their 2FOFC density
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Refine analyze | Num. disordered residues: 17 / Occupancy sum hydrogen: 853 / Occupancy sum non hydrogen: 1102.25 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.88→19.466 Å
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Refine LS restraints |
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