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Yorodumi- PDB-4q0y: Crystal structure of a thioesterase-like protein (CLOSPO_01618) f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q0y | ||||||
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Title | Crystal structure of a thioesterase-like protein (CLOSPO_01618) from Clostridium sporogenes ATCC 15579 at 1.70 A resolution | ||||||
Components | Uncharacterized protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / orphan / Hot Dog/Thioesterase-like fold / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | Immunoglobulin-like - #4400 / Uncharacterised protein Clospo_01618-like / membrane => GO:0016020 / Immunoglobulin-like / Sandwich / Mainly Beta / : / Uncharacterized protein Function and homology information | ||||||
Biological species | Clostridium sporogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a hypothetical protein (CLOSPO_01618) from Clostridium sporogenes ATCC 15579 at 1.70 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 | 4q0y.cif.gz | 181 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q0y.ent.gz | 147.5 KB | Display | PDB format |
PDBx/mmJSON format | 4q0y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q0/4q0y ftp://data.pdbj.org/pub/pdb/validation_reports/q0/4q0y | HTTPS FTP |
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-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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-Components
#1: Protein | Mass: 15578.342 Da / Num. of mol.: 3 / Fragment: UNP residues 31-163 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium sporogenes (bacteria) / Gene: CLOSPO_01618 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: J7SH17 #2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | Sequence details | THIS CONSTRUCT (RESIDUES 31-163) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 31-163) 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: 2.09 Å3/Da / Density % sol: 41.13 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.100M Cadmium Chloride, 30.00% polyethylene glycol 400, 0.1M sodium acetate pH 4.6, 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: BL11-1 / Wavelength: 0.91837,0.97935,0.97901 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2013 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→29.678 Å / Num. obs: 43968 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.92 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 10.41 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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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: 1.7→29.678 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 3.732 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.104 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3.ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3.ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.CADMIUM (CD) FROM THE CRYSTALLIZATION SOLUTION HAS BEEN MODELED IN THE STRUCTURE BASED ON AN ANOMALOUS DIFFERENCE FOURIER MAP. 6.1,2-ETHANEDIOL (EDO) FROM THE CRYOPROTECTANT HAS BEEN MODELED IN THE SOLVENT STRUCTURE. 7.EXPERIMENTAL PHASES IN THE FORM OF HL COEFFICIENTS WERE USED AS RESTRAINTS DURING CRYSTALLOGRAPHIC REFINEMENT.
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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 max: 102.02 Å2 / Biso mean: 24.6016 Å2 / Biso min: 7.7 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→29.678 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 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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