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Yorodumi- PDB-7w44: Complex structure of a leaf-branch compost cutinase variant LCC I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7w44 | ||||||
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Title | Complex structure of a leaf-branch compost cutinase variant LCC ICCG_RIP | ||||||
Components | Leaf-branch compost cutinase | ||||||
Keywords | HYDROLASE / plastic degradation / mutant / catalysis | ||||||
Function / homology | Function and homology information poly(ethylene terephthalate) hydrolase / acetylesterase activity / cutinase activity / cutinase / extracellular region Similarity search - Function | ||||||
Biological species | unidentified prokaryotic organism (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Niu, D. / Zeng, W. / Huang, J.W. / Chen, C.C. / Liu, W.D. / Guo, R.T. | ||||||
Funding support | 1items
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Citation | Journal: Acs Catalysis / Year: 2022 Title: Substrate-Binding Mode of a Thermophilic PET Hydrolase and Engineering the Enzyme to Enhance the Hydrolytic Efficacy. Authors: Zeng, W. / Li, X. / Yang, Y. / Min, J. / Huang, J.-W. / Liu, W. / Niu, D. / Yang, X. / Han, X. / Zhang, L. / Dai, L. / 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 | 7w44.cif.gz | 124.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w44.ent.gz | 94 KB | Display | PDB format |
PDBx/mmJSON format | 7w44.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/7w44 ftp://data.pdbj.org/pub/pdb/validation_reports/w4/7w44 | HTTPS FTP |
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-Related structure data
Related structure data | 7vvcC 7vveC 7w1nC 7w45C 7ds7S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28518.973 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified prokaryotic organism (environmental samples) Plasmid: pET46Ek /LIC / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: G9BY57, cutinase, poly(ethylene terephthalate) hydrolase #2: Chemical | #3: Chemical | ChemComp-IMD / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.56 Å3/Da / Density % sol: 52.03 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 12% w/v PEG 20,000 |
-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: Oct 1, 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: 1.85→24.94 Å / Num. obs: 49376 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.038 / Rrim(I) all: 0.105 / Net I/σ(I): 12.7 / Num. measured all: 336582 / Scaling rejects: 13 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7DS7 Resolution: 1.85→24.94 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.519 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.59 Å2 / Biso mean: 15.706 Å2 / Biso min: 1.62 Å2
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Refinement step | Cycle: final / Resolution: 1.85→24.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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