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Yorodumi- PDB-7f7d: Crystal structure of Non-specific class-C acid phosphatase from S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f7d | ||||||
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Title | Crystal structure of Non-specific class-C acid phosphatase from Sphingobium sp. RSMS bound to Adenosine at pH 5.5 | ||||||
Components | Acid phosphatase | ||||||
Keywords | HYDROLASE / Non specific Phosphatase / Class c / HAD superfamily. | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sphingobium sp. 20006FA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.2 Å | ||||||
Authors | Gaur, N.K. / Kumar, A. / Sunder, S. / Mukhopadhyaya, R. / Makde, R.D. | ||||||
Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f7d.cif.gz | 136.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f7d.ent.gz | 90.7 KB | Display | PDB format |
PDBx/mmJSON format | 7f7d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/7f7d ftp://data.pdbj.org/pub/pdb/validation_reports/f7/7f7d | HTTPS FTP |
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-Related structure data
Related structure data | 7cleC 7f7aC 7f7bC 7f7cC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 31206.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingobium sp. 20006FA (bacteria) / Gene: A8O16_10785 / Production host: Escherichia coli (E. coli) / Strain (production host): BL 21 DE3 / References: UniProt: A0A197BYF0 |
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-Non-polymers , 5 types, 192 molecules
#2: Chemical | ChemComp-ADN / |
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#3: Chemical | ChemComp-PEG / |
#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-PO4 / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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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: 3.16 Å3/Da / Density % sol: 66.63 % / 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: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9795 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 7, 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: 2.2→44.88 Å / Num. obs: 20809 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 23.27 Å2 / CC1/2: 0.997 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.2→2.27 Å / Num. unique obs: 1778 / CC1/2: 0.875 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 2.2→41.98 Å / SU ML: 0.2156 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.7732 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: 25.14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→41.98 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: 4.28133847574 Å / Origin y: -20.8988980116 Å / Origin z: 28.8324085356 Å
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Refinement TLS group | Selection details: all |