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- PDB-7f7b: Crystal structure of Non-specific class-C acid phosphatase from S... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7f7b | ||||||
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Title | Crystal structure of Non-specific class-C acid phosphatase from Sphingobium sp. RSMS bound to BIS-TRIS at pH 5.5 | ||||||
![]() | Acid phosphatase | ||||||
![]() | HYDROLASE / Non specific Phosphatase / Class c / HAD superfamily. | ||||||
Function / homology | 5-nucleotidase lipoprotein e(P4) / Acid phosphatase, class B-like / HAD superfamily, subfamily IIIB (Acid phosphatase) / HAD superfamily / HAD-like superfamily / cell outer membrane / PHOSPHATE ION / Acid phosphatase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Gaur, N.K. / Kumar, A. / Sunder, S. / Mukhopadhyaya, R. / Makde, R.D. | ||||||
![]() | ![]() Title: Non-Specific Class-c acidphosphatase from Sphingobium sp. RSMS Authors: Gaur, N.K. / Kumar, A. / Sunder, S. / Mukhopadhyaya, R. / Makde, R.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.2 KB | Display | ![]() |
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PDB format | ![]() | 87.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1004.3 KB | Display | ![]() |
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Full document | ![]() | 1004.4 KB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 16.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7cleC ![]() 7f7aC ![]() 7f7cC ![]() 7f7dC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31206.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-BTB / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-PO4 / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 66.96 % / Description: Hexagonal Crystals |
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Crystal grow | Temperature: 294 K / Method: microbatch Details: 1M Ammonium sulphate, 0.1 M Bis-tris pH 5.5, 1% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→48.61 Å / Num. obs: 17523 / % possible obs: 99.6 % / Redundancy: 28.4 % / Biso Wilson estimate: 28.72 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2.34→2.42 Å / Rmerge(I) obs: 1.083 / Num. unique obs: 1620 / CC1/2: 0.833 |
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Processing
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 2.34→42.1 Å / SU ML: 0.207 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8649 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.69 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.34→42.1 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 4.26229713283 Å / Origin y: -20.8422341845 Å / Origin z: 28.8956531614 Å
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Refinement TLS group | Selection details: all |