+Open data
-Basic information
Entry | Database: PDB / ID: 7znp | ||||||
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Title | Structure of AmedSP | ||||||
Components | Sucrose phosphorylase | ||||||
Keywords | HYDROLASE / Enzyme / phosphorylase | ||||||
Function / homology | Function and homology information 1,4-alpha-oligoglucan phosphorylase activity / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Alteromonas mediterranea (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Fredslund, F. / Teze, D. / Welner, D.H. | ||||||
Funding support | Denmark, 1items
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Citation | Journal: To Be Published Title: Structure of AmedSP Authors: Fredslund, F. / Teze, D. / Welner, D.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7znp.cif.gz | 247.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7znp.ent.gz | 166.4 KB | Display | PDB format |
PDBx/mmJSON format | 7znp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7znp_validation.pdf.gz | 425.5 KB | Display | wwPDB validaton report |
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Full document | 7znp_full_validation.pdf.gz | 428 KB | Display | |
Data in XML | 7znp_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 7znp_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/7znp ftp://data.pdbj.org/pub/pdb/validation_reports/zn/7znp | HTTPS FTP |
-Related structure data
Related structure data | 1r7aS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Experimental dataset #1 | Data reference: 10.15151/ESRF-DC-1114624654 / Data set type: diffraction image data / Details: ESRF portal - https://data.esrf.fr/doi/ |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 55659.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alteromonas mediterranea (bacteria) / Gene: BM525_11180 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A1J0SGS2 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.43 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 60 % v/v T-mate pH 7.0 / Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 4, 2021 / Details: CRL |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→42.2 Å / Num. obs: 72691 / % possible obs: 99.64 % / Observed criterion σ(F): 0 / Redundancy: 13.7 % / Biso Wilson estimate: 60.64 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1465 / Rpim(I) all: 0.04125 / Rrim(I) all: 0.1523 / Net I/σ(I): 11.14 |
Reflection shell | Resolution: 2.15→2.227 Å / Redundancy: 11.8 % / Num. unique obs: 3658 / CC1/2: 0.313 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1R7A Resolution: 2.15→42.2 Å / SU ML: 0.3295 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.6668 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: 65.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→42.2 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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