+Open data
-Basic information
Entry | Database: PDB / ID: 7v8u | ||||||
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Title | Crystal structure of PsEst3 wild-type | ||||||
Components | Esterase | ||||||
Keywords | HYDROLASE / esterases | ||||||
Function / homology | NITROBENZENE Function and homology information | ||||||
Biological species | Paenibacillus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Son, J. / Kim, H. / Kim, H.W. | ||||||
Funding support | 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 | 7v8u.cif.gz | 70.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7v8u.ent.gz | 50 KB | Display | PDB format |
PDBx/mmJSON format | 7v8u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/7v8u ftp://data.pdbj.org/pub/pdb/validation_reports/v8/7v8u | HTTPS FTP |
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-Related structure data
Related structure data | 7v8vC 7v8wC 7v8xC 1zj4S 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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-Components
#1: Protein | Mass: 29647.170 Da / Num. of mol.: 1 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: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-NBZ / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.3 Å3/Da / Density % sol: 71.37 % |
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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: 0.9796 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.25→48.38 Å / Num. obs: 25533 / % possible obs: 99.9 % / Redundancy: 30.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.014 / Rrim(I) all: 0.083 / Net I/σ(I): 36.6 / Num. measured all: 785631 / Scaling rejects: 190 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1zj4 Resolution: 2.25→48.38 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.23 / 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: 89.86 Å2 / Biso mean: 31.4376 Å2 / Biso min: 11.43 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.25→48.38 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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