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Yorodumi- PDB-2a5m: NMR structure of murine gamma-S crystallin from joint refinement ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a5m | ||||||
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Title | NMR structure of murine gamma-S crystallin from joint refinement with SAXS data | ||||||
Components | Gamma crystallin S | ||||||
Keywords | STRUCTURAL PROTEIN / SAXS / SMALL-ANGLE X-RAY SCATTERING / ALIGNMENT / DEUTERATION / LIQUID CRYSTAL / PF1 / RDC / RESIDUAL DIPOLAR COUPLING / MOLECULAR FRAGMENT REPLACEMENT / MFR | ||||||
Function / homology | Function and homology information structural constituent of eye lens / lens development in camera-type eye / visual perception / morphogenesis of an epithelium Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Grishaev, A. / Wu, J. / Trewhella, J. / Bax, A. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2005 Title: Refinement of Multidomain Protein Structures by Combination of Solution Small-Angle X-ray Scattering and NMR Data. Authors: Grishaev, A. / Wu, J. / Trewhella, J. / Bax, A. #1: Journal: To be Published Title: Solution structure of gamma-S crystallin by molecular fragment replacement NMR Authors: Wu, Z. / Delaglio, F. / Wyatt, K. / Wistow, G. / Bax, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a5m.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2a5m.ent.gz | 947.8 KB | Display | PDB format |
PDBx/mmJSON format | 2a5m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/2a5m ftp://data.pdbj.org/pub/pdb/validation_reports/a5/2a5m | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 20747.271 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crygs / Plasmid: pET17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O35486 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR details | Text: SAXS data was collected on a home-built instrument using a sealed-source X-ray tube and a one-dimensional position sensitive detector. All NMR restraints were taken from entry 1ZWM. |
-Sample preparation
Details | Contents: 0.22 mM gamma-S crystallin, 25 mM imidazole, pH 6.0, 10 mM KCl, 0.04% NaN3, 10 mM DTT, for SAXS data. All NMR conditions as reported for 1ZWM Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 25 mM IMIDAZOLE, 10 mM KCL, 0.04% NaN3 / pH: 6 / Pressure: 1 atm / Temperature: 291.4 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DRX600 with PFG cryoprobe / Manufacturer: Bruker / Model: DRX600 with PFG cryoprobe / Field strength: 600 MHz |
-Processing
NMR software | Name: CNS / Version: 1.0 with an additional SAXS data fitting module Developer: BRUNGER,ADAMS,BONVIN,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE,SIMONSON,WARREN Classification: refinement |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: Experimental NMR data is the same as those in the PDB deposition 1ZWM. SAXS data over the range q = 0.02 to 0.22 A-1 was fitted by an in-house written CNS module. |
NMR representative | Selection criteria: closest to the average |
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 20 / Conformers submitted total number: 20 |