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Yorodumi- PDB-7reo: Crystal structure of an engineered variant of single-chain Penici... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7reo | ||||||
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Title | Crystal structure of an engineered variant of single-chain Penicillin G Acylase from Kluyvera cryocrescens (global hydrolysis Rd3CHis) | ||||||
Components | Penicillin G Acylase | ||||||
Keywords | HYDROLASE / penicillin / acylase | ||||||
Biological species | Kluyvera cryocrescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.812 Å | ||||||
Authors | Orth, P. | ||||||
Citation | Journal: Science / Year: 2022 Title: A chemoenzymatic strategy for site-selective functionalization of native peptides and proteins. Authors: Fryszkowska, A. / An, C. / Alvizo, O. / Banerjee, G. / Canada, K.A. / Cao, Y. / DeMong, D. / Devine, P.N. / Duan, D. / Elgart, D.M. / Farasat, I. / Gauthier, D.R. / Guidry, E.N. / Jia, X. / ...Authors: Fryszkowska, A. / An, C. / Alvizo, O. / Banerjee, G. / Canada, K.A. / Cao, Y. / DeMong, D. / Devine, P.N. / Duan, D. / Elgart, D.M. / Farasat, I. / Gauthier, D.R. / Guidry, E.N. / Jia, X. / Kong, J. / Kruse, N. / Lexa, K.W. / Makarov, A.A. / Mann, B.F. / Milczek, E.M. / Mitchell, V. / Nazor, J. / Neri, C. / Orr, R.K. / Orth, P. / Phillips, E.M. / Riggins, J.N. / Schafer, W.A. / Silverman, S.M. / Strulson, C.A. / Subramanian, N. / Voladri, R. / Yang, H. / Yang, J. / Yi, X. / Zhang, X. / Zhong, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7reo.cif.gz | 180.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7reo.ent.gz | 137.6 KB | Display | PDB format |
PDBx/mmJSON format | 7reo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7reo_validation.pdf.gz | 421.4 KB | Display | wwPDB validaton report |
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Full document | 7reo_full_validation.pdf.gz | 422.9 KB | Display | |
Data in XML | 7reo_validation.xml.gz | 33.6 KB | Display | |
Data in CIF | 7reo_validation.cif.gz | 53.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/re/7reo ftp://data.pdbj.org/pub/pdb/validation_reports/re/7reo | HTTPS FTP |
-Related structure data
Related structure data | 7repC 4pemS 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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Unit cell |
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-Components
#1: Protein | Mass: 86166.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kluyvera cryocrescens (bacteria) / Production host: Escherichia coli (E. coli) |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.88 Å3/Da / Density % sol: 68.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25mM PEG 3350, 200mM MgCl2, 100mM Hepes |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.812→255 Å / Num. obs: 123791 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.999 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 1.812→1.818 Å / Num. unique obs: 1237 / CC1/2: 0.73 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PEM Resolution: 1.812→95.02 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.954 / SU R Cruickshank DPI: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.096 / SU Rfree Blow DPI: 0.091 / SU Rfree Cruickshank DPI: 0.087
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Displacement parameters | Biso max: 90.75 Å2 / Biso mean: 27.94 Å2 / Biso min: 15.52 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.812→95.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.812→1.812 Å / Rfactor Rfree error: 0
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