+Open data
-Basic information
Entry | Database: PDB / ID: 6hsw | ||||||||||||
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Title | A CE15 glucuronoyl esterase from Teredinibacter turnerae T7901 | ||||||||||||
Components | Carbohydrate esterase family 15 domain protein | ||||||||||||
Keywords | HYDROLASE / CE15 / carbohydrate esterase / glucuronoyl esterase / xylan | ||||||||||||
Function / homology | Alpha/Beta hydrolase fold / BROMIDE ION / DI(HYDROXYETHYL)ETHER / Carbohydrate esterase family 15 domain protein Function and homology information | ||||||||||||
Biological species | Teredinibacter turnerae T7901 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.14734381231 Å | ||||||||||||
Authors | Mazurkewich, S. / Lo Leggio, L. / Navarro Poulsen, J.C. / Larsbrink, J. | ||||||||||||
Funding support | Sweden, Denmark, 3items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Structure-function analyses reveal that a glucuronoyl esterase fromTeredinibacter turneraeinteracts with carbohydrates and aromatic compounds. Authors: Arnling Baath, J. / Mazurkewich, S. / Poulsen, J.N. / Olsson, L. / Lo Leggio, L. / Larsbrink, J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hsw.cif.gz | 590.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hsw.ent.gz | 412.3 KB | Display | PDB format |
PDBx/mmJSON format | 6hsw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hsw_validation.pdf.gz | 498.9 KB | Display | wwPDB validaton report |
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Full document | 6hsw_full_validation.pdf.gz | 512.9 KB | Display | |
Data in XML | 6hsw_validation.xml.gz | 55.5 KB | Display | |
Data in CIF | 6hsw_validation.cif.gz | 80.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hs/6hsw ftp://data.pdbj.org/pub/pdb/validation_reports/hs/6hsw | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 48081.297 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Teredinibacter turnerae T7901 (bacteria) Gene: TERTU_0517 / Plasmid: Modified pET28-a / Details (production host): contains TEV protease site / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C5BN23 |
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-Non-polymers , 6 types, 859 molecules
#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
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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: 3.06 Å3/Da / Density % sol: 59.82 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Enzyme mixed 50/50 with reservoir solution containing Morpheus screen solution with 0.09 M halogens (0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide), 0.1 M Buffer system 1 ...Details: Enzyme mixed 50/50 with reservoir solution containing Morpheus screen solution with 0.09 M halogens (0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide), 0.1 M Buffer system 1 (Imidazole; MES) , and 50% v/v Precipitant mix 2 (40% v/v Ethylene glycol; 20 % w/v PEG8000) Temp details: Room Temperature |
-Data collection
Diffraction | Mean temperature: 300 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 26, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.147→44.81 Å / Num. obs: 92246 / % possible obs: 99.79 % / Redundancy: 20.3 % / Biso Wilson estimate: 39.8514198624 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.1978 / Rpim(I) all: 0.04459 / Rrim(I) all: 0.2028 / Net I/σ(I): 13.86 |
Reflection shell | Resolution: 2.147→2.224 Å / Redundancy: 19.6 % / Mean I/σ(I) obs: 1.37 / Num. unique obs: 9051 / CC1/2: 0.634 / Rpim(I) all: 0.4095 / % possible all: 98.96 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.14734381231→44.81 Å / SU ML: 0.254587693418 / Cross valid method: FREE R-VALUE / σ(F): 1.34354230713 / Phase error: 23.1248739467
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.6282588945 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.14734381231→44.81 Å
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Refine LS restraints |
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LS refinement shell |
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