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Yorodumi- PDB-7qef: Crystal structure of para-nitrophenyl-Beta-D-glucuronide bound to... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qef | ||||||
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Title | Crystal structure of para-nitrophenyl-Beta-D-glucuronide bound to a mutant of SN243 (D415A) | ||||||
Components | SN243 | ||||||
Keywords | HYDROLASE / enzyme discovery / carbohydrate-active enzymes (CAZy) / protein engineering / functional metagenomics) | ||||||
Function / homology | ACETATE ION / 4-nitrophenyl beta-D-glucopyranosiduronic acid Function and homology information | ||||||
Biological species | Synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å | ||||||
Authors | Neun, S. / Brear, P. / Campbell, E. / Omari, K. / Wagner, O. / Hyvonen, M. / Hollfelder, F. | ||||||
Funding support | 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qef.cif.gz | 297.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qef.ent.gz | 236.4 KB | Display | PDB format |
PDBx/mmJSON format | 7qef.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/7qef ftp://data.pdbj.org/pub/pdb/validation_reports/qe/7qef | HTTPS FTP |
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-Related structure data
Related structure data | 7qe1SC 7qe2C 7qeaC 7qeeC 7qg4C S: Starting model for refinement 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 81872.844 Da / Num. of mol.: 2 / Mutation: D415A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synthetic construct (others) / Production host: Escherichia coli (E. coli) #3: Sugar | |
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-Non-polymers , 4 types, 211 molecules
#2: Chemical | ChemComp-ACT / | ||||
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#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-SO4 / #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: 2.71 Å3/Da / Density % sol: 54.66 % |
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Crystal grow | Temperature: 283 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 | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.41→85.83 Å / Num. obs: 62881 / % possible obs: 94.5 % / Redundancy: 2.1 % / CC1/2: 0.986 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.101 / Rrim(I) all: 0.16 / Net I/σ(I): 6.5 / Num. measured all: 130173 / Scaling rejects: 2080 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7QE1 Resolution: 2.41→48.081 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 35.53 / Stereochemistry target values: ML
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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 max: 139.82 Å2 / Biso mean: 50.2063 Å2 / Biso min: 19.87 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.41→48.081 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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