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Yorodumi- PDB-2igd: ANISOTROPIC STRUCTURE OF PROTEIN G IGG-BINDING DOMAIN III AT 1.1 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2igd | ||||||
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Title | ANISOTROPIC STRUCTURE OF PROTEIN G IGG-BINDING DOMAIN III AT 1.1 ANGSTROM RESOLUTION | ||||||
Components | PROTEIN G | ||||||
Keywords | IGG-BINDING PROTEIN / ATOMIC RESOLUTION / PROTEIN G / IMMUNOGLOBULIN-BINDING / TRANSMEMBRANE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / INITIAL MODEL WAS PREVIOUSLY OBTAINED STRUCTURE / Resolution: 1.1 Å | ||||||
Authors | Butterworth, S. / Lamzin, V.L. / Wigley, D.B. / Derrick, J.P. / Wilson, K.S. | ||||||
Citation | Journal: To be Published Title: Anisotropic Refinement of a Protein G Domain at 1.1 Angstrom Resolution Authors: Butterworth, S. / Lamzin, V.S. / Wigley, D.B. / Derrick, J.P. / Wilson, K.S. #1: Journal: J.Mol.Biol. / Year: 1994 Title: The Third Igg-Binding Domain from Streptococcal Protein G. An Analysis by X-Ray Crystallography of the Structure Alone and in a Complex with Fab Authors: Derrick, J.P. / Wigley, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2igd.cif.gz | 41.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2igd.ent.gz | 29.2 KB | Display | PDB format |
PDBx/mmJSON format | 2igd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2igd_validation.pdf.gz | 393.6 KB | Display | wwPDB validaton report |
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Full document | 2igd_full_validation.pdf.gz | 393.5 KB | Display | |
Data in XML | 2igd_validation.xml.gz | 6 KB | Display | |
Data in CIF | 2igd_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/2igd ftp://data.pdbj.org/pub/pdb/validation_reports/ig/2igd | HTTPS FTP |
-Related structure data
Related structure data | 1igdS 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: Protein | Mass: 6657.354 Da / Num. of mol.: 1 / Fragment: IMMUNOGLOBULIN-BINDING DOMAIN III Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus sp. (bacteria) / Strain: G148 / Gene: POTENTIAL / Production host: Escherichia coli (E. coli) / Strain (production host): K12 JM101 / References: UniProt: P06654 |
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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: 2.23 Å3/Da / Density % sol: 45 % Description: EXTENSION OF FORMER ISOTROPIC MODEL TO ANISOTROPIC MODEL |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 4.8 Details: CRYSTALS WERE GROWN BY HANGING DROP VAPOUR DIFFUSION FROM 24-26% PEG 4000, 10MM SODIUM ACETATE AT PH 4.8 AND 0.01% SODIUM AZIDE. CELL PARAMETERS ARE NOT THOSE DETERMINED EXPERIMENTALLY. THEY ...Details: CRYSTALS WERE GROWN BY HANGING DROP VAPOUR DIFFUSION FROM 24-26% PEG 4000, 10MM SODIUM ACETATE AT PH 4.8 AND 0.01% SODIUM AZIDE. CELL PARAMETERS ARE NOT THOSE DETERMINED EXPERIMENTALLY. THEY WERE ADJUSTED ON THE BASIS OF THE ENGH & HUBER DICTIONARY AT THE END OF REFINEMENT. THE EXPERIMENTAL ESTIMATES WERE KNOWN TO HAVE POTENTIAL ERRORS DUE TO INACCURACIES IN THE CRYSTAL-TO-DETECTOR AND WAVELENGTH CALIBRATION., vapor diffusion - hanging drop |
-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.72 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1992 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.72 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→10.1 Å / Num. obs: 24145 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 39 |
Reflection shell | Resolution: 1.1→1.12 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.104 / Mean I/σ(I) obs: 12 / Rsym value: 0.104 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: INITIAL MODEL WAS PREVIOUSLY OBTAINED STRUCTURE Starting model: PDB ENTRY 1IGD Resolution: 1.1→10 Å / Num. parameters: 5485 / Num. restraintsaints: 6708 / Cross valid method: FREE R-VALUE / Stereochemistry target values: ENGH & HUBER Details: PROLSQ AND SHELX-93 ALSO USED IN PRELIMINARY STAGES. SHELX-93 AND SHELX-96 REFINEMENT IS AGAINST INTENSITIES.
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Solvent computation | Solvent model: SHELX-96 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 9 / Occupancy sum hydrogen: 409.9 / Occupancy sum non hydrogen: 571.7 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→10 Å
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Refine LS restraints |
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