+Open data
-Basic information
Entry | Database: PDB / ID: 1ab1 | ||||||
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Title | SI FORM CRAMBIN | ||||||
Components | CRAMBIN (SER22/ILE25) | ||||||
Keywords | PLANT SEED PROTEIN / THIONIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Crambe hispanica subsp. abyssinica (Abyssinian crambe) | ||||||
Method | X-RAY DIFFRACTION / ALREADY SOLVED / Resolution: 0.89 Å | ||||||
Authors | Teeter, M.M. / Yamano, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1997 Title: Crystal structure of Ser-22/Ile-25 form crambin confirms solvent, side chain substate correlations. Authors: Yamano, A. / Heo, N.H. / Teeter, M.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ab1.cif.gz | 23.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ab1.ent.gz | 17.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ab1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/1ab1 ftp://data.pdbj.org/pub/pdb/validation_reports/ab/1ab1 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 4728.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Crambe hispanica subsp. abyssinica (Abyssinian crambe) Species: Crambe hispanica / Strain: subsp. abyssinica / References: UniProt: P01542 |
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#2: Chemical | ChemComp-EOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.77 Å3/Da / Density % sol: 30.37 % | ||||||||||||||||||||
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Crystal grow | Method: vapor diffusion - hanging drop - microseeding / pH: 7 Details: HPLC PURIFIED SI-CRAMBIN PROTEIN WAS DISSOLVED AT 25 MG/ML IN 80% ETHANOL/WATER (V/V), AND EQUILIBRATED AGAINS 60% ETHANOL. AFTER 10 DAYS, THE RESERVOIR WAS LOWERED TO 50% AND MICROSEEDED BY ...Details: HPLC PURIFIED SI-CRAMBIN PROTEIN WAS DISSOLVED AT 25 MG/ML IN 80% ETHANOL/WATER (V/V), AND EQUILIBRATED AGAINS 60% ETHANOL. AFTER 10 DAYS, THE RESERVOIR WAS LOWERED TO 50% AND MICROSEEDED BY THE STREAK SEEDING METHOD (CAT WHISKER). AFTER LOWERING THE RESERVOIR TO 45%, GOOD CRYSTALS WERE FORMED., pH 7., vapor diffusion - hanging drop - microseeding | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion / Details: Teeter, M.M., (1979) J. Mol. Biol., 127, 219. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Oct 1, 1992 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 0.89→17.67 Å / Num. obs: 23165 / % possible obs: 88.77 % / Observed criterion σ(I): 0 / Redundancy: 1 % / Rmerge(I) obs: 0.04 / Rsym value: 0.1 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 0.89→0.897 Å / Redundancy: 0.1 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.15 / % possible all: 74.96 |
-Processing
Software |
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Refinement | Method to determine structure: ALREADY SOLVED / Resolution: 0.89→10 Å / Cross valid method: DIFFERENCE DENSITY PEAKS / σ(F): 2 Details: OVERALL WEIGHT WAS 1/(SIGDEL) AND SIGDEL=8-10(SINTH/L-0.166667) THIS STRUCTURE ILLUSTRATES THE CONFIRMATION OF THE ABILITY OF X-RAY DIFFRACTION TO DETECT SUBSTATES. HERE THE SUBSTATES WERE ...Details: OVERALL WEIGHT WAS 1/(SIGDEL) AND SIGDEL=8-10(SINTH/L-0.166667) THIS STRUCTURE ILLUSTRATES THE CONFIRMATION OF THE ABILITY OF X-RAY DIFFRACTION TO DETECT SUBSTATES. HERE THE SUBSTATES WERE PHYSICALLY SEPARATED (TWO SEQUENCE FORMS OF CRAMBIN) AND SEPARATE STRUCTURES DETERMINED. FURTHER SUBSTATES ARE EXTENDED FROM PROTEIN TO SURROUNDING SOLVENT.
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Displacement parameters | Biso mean: 5.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.08 Å / Luzzati d res low obs: 17.6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.89→10 Å
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Refine LS restraints |
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