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Yorodumi- PDB-3f8x: Crystal structure of a putative delta-5-3-ketosteroid isomerase (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f8x | ||||||
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Title | Crystal structure of a putative delta-5-3-ketosteroid isomerase (eca2236) from pectobacterium atrosepticum scri1043 at 1.55 A resolution | ||||||
Components | putative delta-5-3-ketosteroid isomerase | ||||||
Keywords | ISOMERASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / SnoaL-like domain-containing protein Function and homology information | ||||||
Biological species | Pectobacterium atrosepticum SCRI1043 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of putative delta-5-3-ketosteroid isomerase (YP_050331.1) from ERWINIA CAROTOVORA ATROSEPTICA SCRI1043 at 1.55 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f8x.cif.gz | 134.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f8x.ent.gz | 108.7 KB | Display | PDB format |
PDBx/mmJSON format | 3f8x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f8x_validation.pdf.gz | 439.6 KB | Display | wwPDB validaton report |
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Full document | 3f8x_full_validation.pdf.gz | 443 KB | Display | |
Data in XML | 3f8x_validation.xml.gz | 30 KB | Display | |
Data in CIF | 3f8x_validation.cif.gz | 45.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/3f8x ftp://data.pdbj.org/pub/pdb/validation_reports/f8/3f8x | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | AUTHORS STATE THAT STATIC LIGHT SCATTERING MEASUREMENTS INDICATE THAT THE DIMER IS A BIOLOGICAL SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
#1: Protein | Mass: 16550.861 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pectobacterium atrosepticum SCRI1043 (bacteria) Gene: ECA2236, YP_050331.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q6D504 #2: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI | |
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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: 2.26 Å3/Da / Density % sol: 45.64 % Description: THE DATA PROCESSING STATISTICS REPORTED HERE ARE BASED ON TREATING FRIEDEL PAIRS AS SEPARATE REFLECTIONS. |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 20.0000% PEG-6000, 0.1M Citrate pH 5.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97934,0.97922 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 3, 2008 / Details: Flat collimating mirror, toroid focusing mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.55→28.964 Å / Num. obs: 80729 / % possible obs: 94.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.68 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 9.84 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Resolution: 1.55→25.31 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.477 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.078 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.THIS TARGET SHOWS STRUCTURAL SIMILARITY TO KETO-STEROID ISOMERASES BELONGING TO THE NTF2-LIKE FOLD. THE PUTATIVE ACTIVE SITE IS LOCATED IN THE VICINITY OF TYR 59 NEAR SEVERAL UN-EXPLANINED DIFFERENCE ELECTRON DENSITIES THAT WERE NOT MODELED.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.913 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→25.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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