+Open data
-Basic information
Entry | Database: PDB / ID: 7xtw | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | The structure of IsPETase in complex with MHET | ||||||||||||
Components | Poly(ethylene terephthalate) hydrolase | ||||||||||||
Keywords | HYDROLASE / PET hydrolase / PBAT hydrolase / enzyme engineering | ||||||||||||
Function / homology | Function and homology information poly(ethylene terephthalate) hydrolase / acetylesterase activity / carboxylic ester hydrolase activity / : / xenobiotic catabolic process / extracellular region Similarity search - Function | ||||||||||||
Biological species | Ideonella sakaiensis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | ||||||||||||
Authors | Yang, Y. / Jiang, P.C. / Huang, J.-W. / Chen, C.-C. / Guo, R.-T. | ||||||||||||
Funding support | China, 3items
| ||||||||||||
Citation | Journal: Nat Commun / Year: 2023 Title: Complete bio-degradation of poly(butylene adipate-co-terephthalate) via engineered cutinases. Authors: Yang, Y. / Min, J. / Xue, T. / Jiang, P. / Liu, X. / Peng, R. / Huang, J.W. / Qu, Y. / Li, X. / Ma, N. / Tsai, F.C. / Dai, L. / Zhang, Q. / Liu, Y. / Chen, C.C. / Guo, R.T. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7xtw.cif.gz | 72.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7xtw.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 7xtw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xtw_validation.pdf.gz | 694.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7xtw_full_validation.pdf.gz | 696.1 KB | Display | |
Data in XML | 7xtw_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 7xtw_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/7xtw ftp://data.pdbj.org/pub/pdb/validation_reports/xt/7xtw | HTTPS FTP |
-Related structure data
Related structure data | 7xtrC 7xtsC 7xttC 7xtuC 7xtvC 5xg0S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 27366.400 Da / Num. of mol.: 1 / Mutation: R132G,S160A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ideonella sakaiensis (bacteria) / Strain: 201-F6 / Gene: ISF6_4831 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase |
---|
-Non-polymers , 5 types, 262 molecules
#2: Chemical | #3: Chemical | ChemComp-C9C / | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-TRS / | #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: 1.99 Å3/Da / Density % sol: 38.11 % |
---|---|
Crystal grow | Temperature: 298 K / Method: evaporation / pH: 8 Details: 1.6 M Ammonium Sulfate; 0.1 M Tris pH 8.0; 15% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å |
Detector | Type: Bruker PHOTON III / Detector: PIXEL / Date: May 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.34138 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→35.97 Å / Num. obs: 32588 / % possible obs: 99.8 % / Redundancy: 6.12 % / Rmerge(I) obs: 0.0525 / Net I/σ(I): 22.91 |
Reflection shell | Resolution: 1.91→1.94 Å / Redundancy: 5.47 % / Rmerge(I) obs: 0.1421 / Mean I/σ(I) obs: 9.5 / Num. unique obs: 762 / CC1/2: 0.984 / % possible all: 98.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XG0 Resolution: 1.91→35.97 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 11.9 / 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: 58.63 Å2 / Biso mean: 13.1083 Å2 / Biso min: 1.85 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.91→35.97 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23
|