+Open data
-Basic information
Entry | Database: PDB / ID: 1jxy | ||||||
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Title | CRAMBIN MIXED SEQUENCE FORM AT 220 K. PROTEIN/WATER SUBSTATES | ||||||
Components | Crambin | ||||||
Keywords | PLANT PROTEIN / WATER / SUBSTATE / FUNCTION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Crambe hispanica subsp. abyssinica (Abyssinian crambe) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 0.89 Å | ||||||
Authors | Teeter, M.M. / Yamano, A. / Stec, B. / Mohanty, U. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: On the nature of a glassy state of matter in a hydrated protein: Relation to protein function. Authors: Teeter, M.M. / Yamano, A. / Stec, B. / Mohanty, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jxy.cif.gz | 30.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jxy.ent.gz | 20.5 KB | Display | PDB format |
PDBx/mmJSON format | 1jxy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jxy_validation.pdf.gz | 391.1 KB | Display | wwPDB validaton report |
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Full document | 1jxy_full_validation.pdf.gz | 391.2 KB | Display | |
Data in XML | 1jxy_validation.xml.gz | 3.3 KB | Display | |
Data in CIF | 1jxy_validation.cif.gz | 3.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/1jxy ftp://data.pdbj.org/pub/pdb/validation_reports/jx/1jxy | HTTPS FTP |
-Related structure data
Related structure data | 1jxtC 1jxuC 1jxwC 1jxxSC C: citing same article (ref.) 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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Details | Not known but may be monomer |
-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 / |
Sequence details | PRO/SER22:LEU/ILE25 SEQUENCE ISOFORMS ARE MODELLED AS ALTERNATE CONFORMERS IN COORDINATE RECORDS. ...PRO/SER22:LEU/ILE25 SEQUENCE ISOFORMS ARE MODELLED AS ALTERNATE CONFORMERS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.4 Å3/Da / Density % sol: 30 % Description: VALUES OF F/SIGF ARE GIVEN ABOVE RATHER THAN I/SIGI. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: ethanol, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal | *PLUS |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 220 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU AFC-5R / Detector: DIFFRACTOMETER / Date: Dec 21, 1990 / Details: COLLIMATOR |
Radiation | Monochromator: MO / Protocol: SINGLE WAVELENGTH / 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. all: 27080 / Num. obs: 27080 / % possible obs: 74.7 % / Observed criterion σ(I): 0 / Redundancy: 1 % / Biso Wilson estimate: 4.09 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 0.89→0.91 Å / Redundancy: 1 % / Mean I/σ(I) obs: 1.8 / % possible all: 45 |
Reflection | *PLUS |
-Processing
Software |
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Refinement | Starting model: 1JXX, CRAMBIN MIXED FORM AT 200 K. Resolution: 0.89→17.67 Å / Cross valid method: DIFFERENCE DENSITY PEAKS / σ(F): 2 / σ(I): 0 Details: OVERALL WEIGHT WAS 1/(SIGDEL) AND SIGDEL=8-10(SINTH/L-0.166667). WITH PROLSQ, NO RFREE WAS CALCULATED. ********* STEREOCHEMISTRY REMARKS: BECAUSE discretely disordered (MULTIPLE SUBSTATE) ...Details: OVERALL WEIGHT WAS 1/(SIGDEL) AND SIGDEL=8-10(SINTH/L-0.166667). WITH PROLSQ, NO RFREE WAS CALCULATED. ********* STEREOCHEMISTRY REMARKS: BECAUSE discretely disordered (MULTIPLE SUBSTATE) PROTEIN RESIDUES EACH HAVE OCCUPANCY LESS THAN ONE, THEY ARE DIFFICULT TO ACCURATELY REFINE. THE GEOMETRY CAN BE DISTORTED (IS POORLY DETERMINED). IN THE CASE OF THR39, THE BACKBONE IS CLEARLY DISORDERED, WITH VERY SMALL DEVIATIONS BETWEEN SUBSTATES (~0.1 A), AND THAT WAS NOT INCLUDED IN THE MODEL. HENCE THEre may be LARGE ERRORS INVOLVING CA.
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Displacement parameters | Biso mean: 5.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.06 Å / Luzzati d res low obs: 17.67 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.89→17.67 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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