+Open data
-Basic information
Entry | Database: PDB / ID: 7qqi | ||||||
---|---|---|---|---|---|---|---|
Title | Sucrose phosphorylase from Faecalibaculum rodentium | ||||||
Components | Aamy domain-containing protein | ||||||
Keywords | TRANSFERASE / sucrose phosphorylase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Faecalibaculum rodentium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å | ||||||
Authors | Ubiparip, Z. / Capra, N. / Rozeboom, H.J. / Desmet, T. / Thunnissen, A.M.W.H. | ||||||
Funding support | European Union, 1items
| ||||||
Citation | Journal: To Be Published Title: Sucrose phosphorylase from Faecalibaculum rodentium Authors: Ubiparip, Z. / Capra, N. / Rozeboom, H.J. / Thunnissen, A.M.W.H. / Desmet, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7qqi.cif.gz | 365 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7qqi.ent.gz | 287.6 KB | Display | PDB format |
PDBx/mmJSON format | 7qqi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qqi_validation.pdf.gz | 421.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7qqi_full_validation.pdf.gz | 421.1 KB | Display | |
Data in XML | 7qqi_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 7qqi_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/7qqi ftp://data.pdbj.org/pub/pdb/validation_reports/qq/7qqi | HTTPS FTP |
-Related structure data
Related structure data | 6s9vS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 56898.738 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Faecalibaculum rodentium (bacteria) / Gene: AALO17_25870 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A140DYJ4 |
---|---|
#2: Chemical | ChemComp-TRS / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 37 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Protein was concentrated to 30 mg/ml in 25 mM Tris, pH 7.8, 100 mM NaCl. Drops were prepared by mixing protein and reservoir solution at a 1:1 volume ratio. Composition reservoir solution: 1 ...Details: Protein was concentrated to 30 mg/ml in 25 mM Tris, pH 7.8, 100 mM NaCl. Drops were prepared by mixing protein and reservoir solution at a 1:1 volume ratio. Composition reservoir solution: 1 M Na citrate, 0.1 M Tris, pH 7.0, 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 25, 2020 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.965459 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.36→46 Å / Num. obs: 95834 / % possible obs: 99.7 % / Redundancy: 5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.056 / Rrim(I) all: 0.095 / Net I/σ(I): 10.7 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6S9V Resolution: 1.36→46 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / SU B: 3.355 / SU ML: 0.056 / Cross valid method: FREE R-VALUE / ESU R: 0.061 / ESU R Free: 0.057 Details: Hydrogens have been added in their riding positions
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.554 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.36→46 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|