+Open data
-Basic information
Entry | Database: PDB / ID: 7v8v | ||||||
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Title | Crystal structure of PsEst3 S128A mutant | ||||||
Components | esterase | ||||||
Keywords | HYDROLASE / esterases | ||||||
Biological species | Paenibacillus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Son, J. / Kim, H. / Kim, H.W. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Iucrj / Year: 2023 Title: Structural and biochemical insights into PsEst3, a new GHSR-type esterase obtained from Paenibacillus sp. R4. Authors: Son, J. / Choi, W. / Kim, H. / Kim, M. / Lee, J.H. / Shin, S.C. / Kim, H.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7v8v.cif.gz | 67.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7v8v.ent.gz | 48.1 KB | Display | PDB format |
PDBx/mmJSON format | 7v8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/7v8v ftp://data.pdbj.org/pub/pdb/validation_reports/v8/7v8v | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29631.170 Da / Num. of mol.: 1 / Mutation: S128A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenibacillus sp. (bacteria) / Production host: Escherichia coli (E. coli) |
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#2: Water | ChemComp-HOH / |
Sequence details | this protein is S128A mutant |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.16 Å3/Da / Density % sol: 70.45 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.1 M bis-tris pH 6.5, 2.0 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→47.87 Å / Num. obs: 20538 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.023 / Rrim(I) all: 0.085 / Net I/σ(I): 26.9 / Num. measured all: 279175 / Scaling rejects: 60 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7V8U Resolution: 2.4→34.83 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.93 / 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: 102.89 Å2 / Biso mean: 45.0932 Å2 / Biso min: 22.65 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→34.83 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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