+Open data
-Basic information
Entry | Database: PDB / ID: 1lr3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of thaumatin at high hydrostatic pressure | ||||||
Components | Thaumatin I | ||||||
Keywords | PLANT PROTEIN / Taste-modifying protein / sweet protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Charron, C. / Kadri, A. / Robert, M.C. / Capelle, B. / Giege, R. / Lorber, B. | ||||||
Citation | Journal: J.CRYST.GROWTH / Year: 2002 Title: X-ray diffraction properties of protein crystals prepared in agarose gel under hydrostatic pressure. Authors: Charron, C. / Robert, M.-C. / Capelle, B. / Kadri, A. / Jenner, G. / Giege, R. / Lorber, B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1lr3.cif.gz | 51.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1lr3.ent.gz | 40.1 KB | Display | PDB format |
PDBx/mmJSON format | 1lr3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lr3_validation.pdf.gz | 438.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1lr3_full_validation.pdf.gz | 440.1 KB | Display | |
Data in XML | 1lr3_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 1lr3_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/1lr3 ftp://data.pdbj.org/pub/pdb/validation_reports/lr/1lr3 | HTTPS FTP |
-Related structure data
Related structure data | 1thwS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22227.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thaumatococcus daniellii (katemfe) / References: UniProt: P02883 |
---|---|
#2: Chemical | ChemComp-TLA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.41 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: small tubes / pH: 6.5 / Details: tartrate, pH 6.5, SMALL TUBES, temperature 293.0K | ||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9474 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 24, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9474 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 24544 / Num. obs: 24544 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Rsym value: 0.03 |
Reflection shell | Resolution: 1.8→1.86 Å / Num. unique all: 2006 / Rsym value: 0.057 / % possible all: 100 |
Reflection | *PLUS Rmerge(I) obs: 0.03 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.057 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1THW Resolution: 1.8→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.86 Å
|