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Yorodumi- PDB-7ypn: Crystal structure of transaminase CC1012 mutant M9 complexed with PLP -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ypn | ||||||
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Title | Crystal structure of transaminase CC1012 mutant M9 complexed with PLP | ||||||
Components | Aspartate aminotransferase family protein | ||||||
Keywords | TRANSFERASE / Complex / Tranaminase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Caulobacter sp. D5 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.049 Å | ||||||
Authors | Yang, L. / Wang, H. / Wei, D. | ||||||
Funding support | China, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2022 Title: Mechanism-Guided Computational Design of omega-Transaminase by Reprograming of High-Energy-Barrier Steps. Authors: Yang, L. / Zhang, K. / Xu, M. / Xie, Y. / Meng, X. / Wang, H. / Wei, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ypn.cif.gz | 199.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ypn.ent.gz | 155.6 KB | Display | PDB format |
PDBx/mmJSON format | 7ypn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ypn_validation.pdf.gz | 469.7 KB | Display | wwPDB validaton report |
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Full document | 7ypn_full_validation.pdf.gz | 471.4 KB | Display | |
Data in XML | 7ypn_validation.xml.gz | 37.6 KB | Display | |
Data in CIF | 7ypn_validation.cif.gz | 55.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/7ypn ftp://data.pdbj.org/pub/pdb/validation_reports/yp/7ypn | HTTPS FTP |
-Related structure data
Related structure data | 7ypmSC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 52067.395 Da / Num. of mol.: 2 Mutation: Q25F, D44E, M60W, W64F, Y138F, P192Q, I266A, T377V, A448R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caulobacter sp. D5 (bacteria) / Gene: DMC18_08975 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A318BC23 #2: Chemical | #3: Chemical | ChemComp-EDO / | #4: Chemical | ChemComp-PEG / | #5: 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: 2.05 Å3/Da / Density % sol: 40.08 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.69 Details: 100 mM Tris-HCl, pH 8.69, LiCl, 0.8 M, PEG 4000, 29% (w/v) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.049→50 Å / Num. obs: 52548 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 24.24 Å2 / CC1/2: 0.8 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.05→2.09 Å / Num. unique obs: 2588 / CC1/2: 0.816 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7YPM Resolution: 2.049→39.44 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.57 / 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: 62.95 Å2 / Biso mean: 24.4227 Å2 / Biso min: 12.11 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.049→39.44 Å
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Refine LS restraints |
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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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