[English] 日本語
Yorodumi- PDB-3qac: Structure of amaranth 11S proglobulin seed storage protein from A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qac | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of amaranth 11S proglobulin seed storage protein from Amaranthus hypochondriacus L. | ||||||
Components | 11S globulin seed storage protein | ||||||
Keywords | PLANT PROTEIN / 11S seed storage protein (globulins) family / seed storage protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Amaranthus hypochondriacus (grain amaranth) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.275 Å | ||||||
Authors | Tandang-Silvas, M.R. / Carrazco-Pena, L. / Barba de la Rosa, A.P. / Osuna-Castro, J.A. / Utsumi, S. / Mikami, B. / Maruyama, N. | ||||||
Citation | Journal: To be Published Title: Structure of amaranth 11S proglobulin, a major seed storage protein from Amaranthus hypochondriacus L. Authors: Tandang-Silvas, M.R. / Carrazco-Pena, L. / Barba de la Rosa, A.P. / Osuna-Castro, J.A. / Utsumi, S. / Mikami, B. / Maruyama, N. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: Expression, purification and preliminary crystallization of amaranth 11S proglobulin seed storage protein from Amaranthus hypochondriacus L. Authors: Tandang-Silvas, M.R. / Carrazco-Pena, L. / Barba de la Rosa, A.P. / Osuna-Castro, J.A. / Utsumi, S. / Mikami, B. / Maruyama, N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3qac.cif.gz | 89.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3qac.ent.gz | 66.2 KB | Display | PDB format |
PDBx/mmJSON format | 3qac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/3qac ftp://data.pdbj.org/pub/pdb/validation_reports/qa/3qac | HTTPS FTP |
---|
-Related structure data
Related structure data | 2e9qS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 52721.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amaranthus hypochondriacus (grain amaranth) Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami(DE3) / References: UniProt: Q38712 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 32.02 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 16% PEG3350, 200mM ammonium formate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 5, 2010 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.275→50 Å / Num. all: 17239 / Num. obs: 17067 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 47.1 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 4 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 4.01 / Num. unique all: 860 / % possible all: 99.3 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2E9Q Resolution: 2.275→28.468 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7811 / SU ML: 0.34 / σ(F): 1.34 / Phase error: 28.43 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.331 Å2 / ksol: 0.328 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.18 Å2 / Biso mean: 49.2937 Å2 / Biso min: 25.93 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.275→28.468 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
|