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Yorodumi- PDB-8h7c: Crystal structure of a de novo enzyme, ferric enterobactin estera... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8h7c | ||||||||||||
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Title | Crystal structure of a de novo enzyme, ferric enterobactin esterase Syn-F4 (K4T) - Pt derivative | ||||||||||||
Components | De novo ferric enterobactin esterase Syn-F4 | ||||||||||||
Keywords | DE NOVO PROTEIN / Binary patterned library / De novo enzyme / Dimeric 4-helix bundle / Ferric enterobactin esterase | ||||||||||||
Function / homology | ACETATE ION / TETRACHLOROPLATINATE(II) / : Function and homology information | ||||||||||||
Biological species | synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å | ||||||||||||
Authors | Kurihara, K. / Umezawa, K. / Donnelly, A.E. / Hecht, M.H. / Arai, R. | ||||||||||||
Funding support | Japan, United States, 3items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2023 Title: Crystal structure and activity of a de novo enzyme, ferric enterobactin esterase Syn-F4. Authors: Kurihara, K. / Umezawa, K. / Donnelly, A.E. / Sperling, B. / Liao, G. / Hecht, M.H. / Arai, R. #1: Journal: Nat Chem Biol / Year: 2018 Title: A de novo enzyme catalyzes a life-sustaining reaction in Escherichia coli. Authors: Donnelly, A.E. / Murphy, G.S. / Digianantonio, K.M. / Hecht, M.H. #2: Journal: Protein Sci / Year: 2015 Title: Divergent evolution of a bifunctional de novo protein. Authors: Smith, B.A. / Mularz, A.E. / Hecht, M.H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h7c.cif.gz | 55.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h7c.ent.gz | 38.4 KB | Display | PDB format |
PDBx/mmJSON format | 8h7c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/8h7c ftp://data.pdbj.org/pub/pdb/validation_reports/h7/8h7c | HTTPS FTP |
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-Related structure data
Related structure data | 8h7dC 8h7eC 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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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 12481.063 Da / Num. of mol.: 2 / Mutation: K4T Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Gene: synF4 / Plasmid: pCA24N / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: iron(III)-enterobactin esterase |
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-Non-polymers , 5 types, 45 molecules
#2: Chemical | ChemComp-PT / |
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#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-ACT / |
#5: Chemical | ChemComp-PC4 / |
#6: Water | ChemComp-HOH / |
-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: 1.91 Å3/Da / Density % sol: 35.44 % / Description: Plate-like crystal |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.9 Details: 0.1M Tris, 0.2M ammonium acetate, 8% PEG 3350 (soaking in 10mM K2PtCl4 for 1 day) |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1.073, 1.069, 1.045 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 18, 2018 / Details: Focusing Mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.15→50 Å / Num. obs: 10257 / % possible obs: 95.5 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.022 / Rrim(I) all: 0.078 / Χ2: 0.964 / Net I/σ(I): 5.5 / Num. measured all: 119496 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.919 / SU B: 7.865 / SU ML: 0.196 / SU R Cruickshank DPI: 0.4453 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.445 / ESU R Free: 0.265 / 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: 110.7 Å2 / Biso mean: 35.834 Å2 / Biso min: 10.46 Å2
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Refinement step | Cycle: final / Resolution: 2.15→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.151→2.207 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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