+Open data
-Basic information
Entry | Database: PDB / ID: 7qe2 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of D-glucuronic acid bound to SN243 | ||||||
Components | SN243 | ||||||
Keywords | HYDROLASE / enzyme discovery / carbohydrate-active enzymes (CAZy) / protein engineering / functional metagenomics) | ||||||
Function / homology | ACETATE ION / beta-D-glucopyranuronic acid Function and homology information | ||||||
Biological species | unidentified (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Neun, S. / Brear, P. / Campbell, E. / Omari, K. / Wagner, O. / Hyvonen, M. / Hollfelder, F. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2022 Title: Functional metagenomic screening identifies an unexpected beta-glucuronidase. Authors: Neun, S. / Brear, P. / Campbell, E. / Tryfona, T. / El Omari, K. / Wagner, A. / Dupree, P. / Hyvonen, M. / Hollfelder, F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7qe2.cif.gz | 304.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7qe2.ent.gz | 241.2 KB | Display | PDB format |
PDBx/mmJSON format | 7qe2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qe2_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7qe2_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7qe2_validation.xml.gz | 56.3 KB | Display | |
Data in CIF | 7qe2_validation.cif.gz | 79.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/7qe2 ftp://data.pdbj.org/pub/pdb/validation_reports/qe/7qe2 | HTTPS FTP |
-Related structure data
Related structure data | 7qe1SC 7qeaC 7qeeC 7qefC 7qg4C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
|
-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 81916.852 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli BL21(DE3) (bacteria) #2: Sugar | |
---|
-Non-polymers , 4 types, 407 molecules
#3: Chemical | ChemComp-ACT / | ||||
---|---|---|---|---|---|
#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-SO4 / #6: 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: 2.71 Å3/Da / Density % sol: 54.69 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 0.01 M ZnSO4 and 25% PEG MME 550 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 23, 2021 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.15→48.31 Å / Num. obs: 91233 / % possible obs: 97.3 % / Redundancy: 3.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.067 / Rrim(I) all: 0.126 / Net I/σ(I): 7.1 / Num. measured all: 325221 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.7 %
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7QE1 Resolution: 2.15→48.306 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.1 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 133.75 Å2 / Biso mean: 57.726 Å2 / Biso min: 34.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.15→48.306 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|