+Open data
-Basic information
Entry | Database: PDB / ID: 7epn | |||||||||
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Title | Ketosteroid Isomerase KSI native | |||||||||
Components | SnoaL-like domain-containing protein | |||||||||
Keywords | ISOMERASE / Kemp elimination / MsKSI / Mycobacterium smegmatis / Crystal structure. | |||||||||
Function / homology | SnoaL-like domain / SnoaL-like domain / NTF2-like domain superfamily / SnoaL-like domain-containing protein Function and homology information | |||||||||
Biological species | Mycolicibacterium smegmatis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Liang, Y. / Zhang, Q. / Bartlam, M. | |||||||||
Funding support | China, 2items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2021 Title: Structural characterization and Kemp eliminase activity of the Mycobacterium smegmatis Ketosteroid Isomerase. Authors: Liang, Y. / Li, W. / Liang, H. / Lou, X. / Liu, R. / Zhang, Q. / Bartlam, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7epn.cif.gz | 141.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7epn.ent.gz | 92.4 KB | Display | PDB format |
PDBx/mmJSON format | 7epn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7epn_validation.pdf.gz | 432.5 KB | Display | wwPDB validaton report |
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Full document | 7epn_full_validation.pdf.gz | 433.6 KB | Display | |
Data in XML | 7epn_validation.xml.gz | 12 KB | Display | |
Data in CIF | 7epn_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/7epn ftp://data.pdbj.org/pub/pdb/validation_reports/ep/7epn | HTTPS FTP |
-Related structure data
Related structure data | 7epoC 3grdS 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: 16394.328 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: MSMEI_6677 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I7FVV8 #2: Water | ChemComp-HOH / | |
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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: 2.35 Å3/Da / Density % sol: 47.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.5 Details: 0.2 M Sodium acetate trihydrate, 0.1M Tris, pH 8.5, 30% PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 25005 / % possible obs: 99.4 % / Redundancy: 13 % / Biso Wilson estimate: 17.14 Å2 / Rpim(I) all: 0.019 / Net I/σ(I): 35.78 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 13.2 % / Mean I/σ(I) obs: 20.59 / Num. unique obs: 1237 / Rpim(I) all: 0.042 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GRD Resolution: 1.9→42.8 Å / SU ML: 0.1833 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.4408 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 20.59 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→42.8 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 30.8392479715 Å / Origin y: 14.1760496534 Å / Origin z: -16.2592277046 Å
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Refinement TLS group | Selection details: all |