[English] 日本語
Yorodumi- PDB-6vj7: Crystal structure of red kidney bean purple acid phosphatase in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vj7 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of red kidney bean purple acid phosphatase in complex with adenosine 5'-(beta,gamma imido)triphosphate | ||||||||||||
Components | Fe(3+)-Zn(2+) purple acid phosphatase | ||||||||||||
Keywords | METAL BINDING PROTEIN / Hydrolase / Purple acid phosphatase / metallohydrolases / catalysis / phytase / ATPase / agricultural biotechnology | ||||||||||||
Function / homology | Function and homology information acid phosphatase / acid phosphatase activity / ferric iron binding / zinc ion binding / extracellular region Similarity search - Function | ||||||||||||
Biological species | Phaseolus vulgaris (French bean) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||||||||
Authors | Feder, D. / Schenk, G. / Guddat, L.W. / McGeary, R.P. / Mitic, N. / Furtado, A. / Schulz, B.L. / Henry, R.J. / Schmidt, S. | ||||||||||||
Funding support | Australia, 2items
| ||||||||||||
Citation | Journal: Plant Sci. / Year: 2020 Title: Structural elements that modulate the substrate specificity of plant purple acid phosphatases: Avenues for improved phosphorus acquisition in crops. Authors: Feder, D. / McGeary, R.P. / Mitic, N. / Lonhienne, T. / Furtado, A. / Schulz, B.L. / Henry, R.J. / Schmidt, S. / Guddat, L.W. / Schenk, G. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6vj7.cif.gz | 398.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6vj7.ent.gz | 322.7 KB | Display | PDB format |
PDBx/mmJSON format | 6vj7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vj7_validation.pdf.gz | 949.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6vj7_full_validation.pdf.gz | 964.7 KB | Display | |
Data in XML | 6vj7_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 6vj7_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/6vj7 ftp://data.pdbj.org/pub/pdb/validation_reports/vj/6vj7 | HTTPS FTP |
-Related structure data
Related structure data | 6py9C 4dhlS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 49555.398 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Phaseolus vulgaris (French bean) / References: UniProt: P80366, acid phosphatase |
---|
-Sugars , 6 types, 15 molecules
#2: Polysaccharide | beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||||||
---|---|---|---|---|---|---|---|---|---|
#3: Polysaccharide | #4: Polysaccharide | beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Polysaccharide | #6: Polysaccharide | #13: Sugar | ChemComp-NAG / |
-Non-polymers , 11 types, 859 molecules
#7: Chemical | ChemComp-ZN / #8: Chemical | ChemComp-FE / #9: Chemical | ChemComp-SO4 / #10: Chemical | ChemComp-GOL / #11: Chemical | ChemComp-EDO / #12: Chemical | ChemComp-PGE / #14: Chemical | #15: Chemical | #16: Chemical | #17: Chemical | ChemComp-IPA / | #18: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.19 % / Description: Hexagonal |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 2.3 M ammonium sulfate, 0.1 M sodium acetate, pH 4.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 10, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40.76 Å / Num. obs: 63465 / % possible obs: 74.9 % / Redundancy: 1.62 % / Biso Wilson estimate: 36.25 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 1.36 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1835 / Χ2: 1.11 / % possible all: 50.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DHL Resolution: 2.6→40.76 Å / SU ML: 0.373 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.327 Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→40.76 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|