+Open data
-Basic information
Entry | Database: PDB / ID: 1krl | ||||||
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Title | Crystal Structure of Racemic DL-monellin in P-1 | ||||||
Components |
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Keywords | PLANT PROTEIN / alpha-beta | ||||||
Function / homology | Function and homology information Helix Hairpins - #2000 / N-terminal domain of TfIIb - #130 / Monellin, A chain / Monellin, A chain superfamily / Monellin, B chain / Monellin / Monellin / N-terminal domain of TfIIb / Cystatin superfamily / Other non-globular ...Helix Hairpins - #2000 / N-terminal domain of TfIIb - #130 / Monellin, A chain / Monellin, A chain superfamily / Monellin, B chain / Monellin / Monellin / N-terminal domain of TfIIb / Cystatin superfamily / Other non-globular / Helix Hairpins / Helix non-globular / Special Similarity search - Domain/homology | ||||||
Biological species | Dioscoreophyllum cumminsii (serendipity berry) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Hung, L.W. / Kohmura, M. / Ariyoshi, Y. / Kim, S.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Structural differences in D and L-monellin in the crystals of racemic mixture. Authors: Hung, L.W. / Kohmura, M. / Ariyoshi, Y. / Kim, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1krl.cif.gz | 55.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1krl.ent.gz | 40.1 KB | Display | PDB format |
PDBx/mmJSON format | 1krl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/1krl ftp://data.pdbj.org/pub/pdb/validation_reports/kr/1krl | 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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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 5259.993 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Dioscoreophyllum cumminsii (serendipity berry) References: UniProt: P02881 #2: Protein/peptide | Mass: 5841.647 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry) References: UniProt: P02882 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.68 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: Phosphate buffer, PEG8000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 4K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 10, 1994 / Details: Yale mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25 Å / Num. all: 36070 / Num. obs: 31453 / % possible obs: 87.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 10.3 Å2 / Rmerge(I) obs: 0.046 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 2 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 2.3 / Num. unique all: 31453 / % possible all: 41.8 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 31489 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Single Chain Monellin Resolution: 1.9→6 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 267815.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 129.389 Å2 / ksol: 0.795121 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.01 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 6 Å / Num. reflection all: 26867 / Num. reflection obs: 23409 / σ(F): 2 / % reflection Rfree: 9.8 % / Rfactor obs: 0.255 / Rfactor Rfree: 0.298 | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.308 / % reflection Rfree: 9.5 % / Rfactor Rwork: 0.306 |