+Open data
-Basic information
Entry | Database: PDB / ID: 7xtv | ||||||||||||
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Title | The structure of MHET-bound TfCut S130A | ||||||||||||
Components | alpha/beta hydrolase | ||||||||||||
Keywords | HYDROLASE / PET hydrolase / PBAT hydrolase / enzyme engineering / cutinase | ||||||||||||
Function / homology | ACETATE ION / 4-(2-hydroxyethyloxycarbonyl)benzoic acid / DI(HYDROXYETHYL)ETHER Function and homology information | ||||||||||||
Biological species | Thermobifida fusca (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||||||||
Authors | Yang, Y. / Jiang, P.C. / Huang, J.-W. / Chen, C.-C. / Guo, R.-T. | ||||||||||||
Funding support | China, 3items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xtv.cif.gz | 228.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xtv.ent.gz | 181 KB | Display | PDB format |
PDBx/mmJSON format | 7xtv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xtv_validation.pdf.gz | 877.7 KB | Display | wwPDB validaton report |
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Full document | 7xtv_full_validation.pdf.gz | 873.8 KB | Display | |
Data in XML | 7xtv_validation.xml.gz | 47.1 KB | Display | |
Data in CIF | 7xtv_validation.cif.gz | 68.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/7xtv ftp://data.pdbj.org/pub/pdb/validation_reports/xt/7xtv | HTTPS FTP |
-Related structure data
Related structure data | 7xtrC 7xtsC 7xttC 7xtuC 7xtwC 5zoaS 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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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 28302.760 Da / Num. of mol.: 4 / Mutation: S130A Source method: isolated from a genetically manipulated source Details: GB:PZN61876.1 / Source: (gene. exp.) Thermobifida fusca (bacteria) / Gene: cut-2.KW3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: cutinase |
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-Non-polymers , 6 types, 883 molecules
#2: Chemical | #3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-GOL / | #5: Chemical | #6: Chemical | ChemComp-SO4 / #7: Water | ChemComp-HOH / | |
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-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: 2.64 Å3/Da / Density % sol: 53.46 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 4 Details: 4% v/v PEG200; 0.8 M lithium sulfate; 0.1 M sodium acetate pH4.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å |
Detector | Type: Bruker PHOTON III / Detector: PIXEL / Date: Apr 22, 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: 2.31→45.74 Å / Num. obs: 100354 / % possible obs: 99.6 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.0692 / Net I/σ(I): 14.96 |
Reflection shell | Resolution: 2.31→2.35 Å / Redundancy: 3.01 % / Rmerge(I) obs: 0.1601 / Mean I/σ(I) obs: 4.66 / Num. unique obs: 2675 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5zoa Resolution: 2.31→42 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.44 / 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: 93.19 Å2 / Biso mean: 17.3015 Å2 / Biso min: 4.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.31→42 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27
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