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Yorodumi- PDB-3kkg: Crystal structure of Putative SnoaL-like polyketide cyclase (YP_5... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kkg | ||||||
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Title | Crystal structure of Putative SnoaL-like polyketide cyclase (YP_509242.1) from Jannaschia Sp. CCS1 at 1.40 A resolution | ||||||
Components | Putative SnoaL-like polyketide cyclase | ||||||
Keywords | LYASE / Putative SnoaL-like polyketide cyclase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Jannaschia sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Putative SnoaL-like polyketide cyclase (YP_509242.1) from Jannaschia Sp. CCS1 at 1.40 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 | 3kkg.cif.gz | 47.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kkg.ent.gz | 36.1 KB | Display | PDB format |
PDBx/mmJSON format | 3kkg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kkg_validation.pdf.gz | 435.4 KB | Display | wwPDB validaton report |
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Full document | 3kkg_full_validation.pdf.gz | 435.3 KB | Display | |
Data in XML | 3kkg_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 3kkg_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/3kkg ftp://data.pdbj.org/pub/pdb/validation_reports/kk/3kkg | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-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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Details | ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. |
-Components
#1: Protein | Mass: 16248.476 Da / Num. of mol.: 1 / Fragment: sequence database residues 28-172 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Jannaschia sp. (bacteria) / Strain: CCS1 / Gene: Jann_1300 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q28SU5 | ||||||
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#2: Chemical | ChemComp-CL / | ||||||
#3: Chemical | #4: Chemical | ChemComp-PGE / | #5: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT (28-172) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (28-172) WAS EXPRESSED WITH A PURIFICATI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2000M CaCl2, 28.0000% PEG-400, 0.1M HEPES pH 7.5, 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: 0.91162,0.97925,0.97911 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 30, 2009 / 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: 1.4→29.21 Å / Num. obs: 34674 / % possible obs: 98.4 % / Redundancy: 9.5 % / Biso Wilson estimate: 18.347 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 18.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.4→29.21 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 0.22 / SU B: 2.105 / SU ML: 0.043 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.06 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. PEG400 FRAGMENTS (PEG AND PGE) AND A CHLORIDE ION WERE MODELED BASED ON CRYSTALLIZATION CONDITIONS. 5. UNEXPLAINED ELECTRON DENSITY NEAR RESIDUE 34 WAS 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.77 Å2 / Biso mean: 23.155 Å2 / Biso min: 11.37 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→29.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 26.1092 Å / Origin y: 28.7992 Å / Origin z: 8.3087 Å
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