+Open data
-Basic information
Entry | Database: PDB / ID: 1jxu | ||||||
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Title | CRAMBIN MIXED SEQUENCE FORM AT 240 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: 0.99 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 | 1jxu.cif.gz | 27.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jxu.ent.gz | 18.5 KB | Display | PDB format |
PDBx/mmJSON format | 1jxu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jxu_validation.pdf.gz | 381.3 KB | Display | wwPDB validaton report |
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Full document | 1jxu_full_validation.pdf.gz | 381.3 KB | Display | |
Data in XML | 1jxu_validation.xml.gz | 3 KB | Display | |
Data in CIF | 1jxu_validation.cif.gz | 3.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/1jxu ftp://data.pdbj.org/pub/pdb/validation_reports/jx/1jxu | HTTPS FTP |
-Related structure data
Related structure data | 1jxtC 1jxwC 1jxxC 1jxySC 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 | Biological assembly not known. |
-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 | sequence PRO/SER22:LEU/ILE25 SEQUENCE ISOFORMS ARE MODELLED AS ALTERNATE CONFORMERS IN COORDINATE ...sequence 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: 240 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 25, 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: 0.99→17.67 Å / Num. all: 7272 / Num. obs: 7272 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1 % / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 0.99→1 Å / Redundancy: 1 % / Mean I/σ(I) obs: 4.4 / % possible all: 0.162 |
Reflection | *PLUS % possible obs: 92 % / Rmerge(I) obs: 0.139 |
-Processing
Software |
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Refinement | Starting model: 1JXY. CRAMBIN MIXED ISOFORM AT 220 K. Resolution: 0.99→17.67 Å / Cross valid method: DIFFERENCE DENSITY PEAKS / σ(F): 2 / σ(I): 2 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).
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Displacement parameters | Biso mean: 5.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.06 Å / Luzzati d res low obs: 17.67 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.99→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 / Rfactor obs: 0.09 / Rfactor Rwork: 0.09 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 5.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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