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Yorodumi- PDB-2qmt: Crystal Polymorphism of Protein GB1 Examined by Solid-state NMR a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qmt | ||||||
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Title | Crystal Polymorphism of Protein GB1 Examined by Solid-state NMR and X-ray Diffraction | ||||||
Components | Immunoglobulin G-binding protein G | ||||||
Keywords | IMMUNE SYSTEM / immunglobulin binding domain / thermostable | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å | ||||||
Authors | Frericks Schmidt, H.L. / Sperling, L.J. / Gao, Y.G. / Wylie, B.J. / Boettcher, J.M. / Wilson, S.R. / Rienstra, C.M. | ||||||
Citation | Journal: J.Phys.Chem.B / Year: 2007 Title: Crystal Polymorphism of Protein GB1 Examined by Solid-State NMR Spectroscopy and X-ray Diffraction. Authors: Frericks Schmidt, H.L. / Sperling, L.J. / Gao, Y.G. / Wylie, B.J. / Boettcher, J.M. / Wilson, S.R. / Rienstra, C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qmt.cif.gz | 27.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qmt.ent.gz | 16.8 KB | Display | PDB format |
PDBx/mmJSON format | 2qmt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qmt_validation.pdf.gz | 455.3 KB | Display | wwPDB validaton report |
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Full document | 2qmt_full_validation.pdf.gz | 455.9 KB | Display | |
Data in XML | 2qmt_validation.xml.gz | 7 KB | Display | |
Data in CIF | 2qmt_validation.cif.gz | 9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/2qmt ftp://data.pdbj.org/pub/pdb/validation_reports/qm/2qmt | HTTPS FTP |
-Related structure data
Related structure data | 1pgaS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Antibody | Mass: 6228.809 Da / Num. of mol.: 1 Fragment: immunoglobulin beta 1 binding domain (residues 303-357) Mutation: T2Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Description: synthesized plasmid, prepared according to Smith, C., Withka, J., and Regan, L. Biochemistry 1994, 33, 5510-5517, expressing protein identical in sequence and structure to the IgG beta 1 ...Description: synthesized plasmid, prepared according to Smith, C., Withka, J., and Regan, L. Biochemistry 1994, 33, 5510-5517, expressing protein identical in sequence and structure to the IgG beta 1 binding domain of protein G of Streptococcus areus Gene: spg / 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: Chemical | ChemComp-PO4 / | ||
#3: Chemical | ChemComp-MRD / ( | ||
#4: Chemical | #5: 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: 2.24 Å3/Da / Density % sol: 45 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 50 mM NaCl, 50% MPD, 6% IPA, 25 mM Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 1, 2005 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→50 Å / Num. all: 25387 / Num. obs: 25051 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Rmerge(I) obs: 0.062 |
Reflection shell | Resolution: 1.05→1.09 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.238 / Num. unique all: 1340 / % possible all: 64.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PGA Resolution: 1.05→10 Å / Isotropic thermal model: Isotropic / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 14.491 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.05→10 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 1.05 Å
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