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Yorodumi- PDB-3oqp: Crystal structure of a putative isochorismatase (Bxe_A0706) from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oqp | ||||||
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Title | Crystal structure of a putative isochorismatase (Bxe_A0706) from BURKHOLDERIA XENOVORANS LB400 at 1.22 A resolution | ||||||
Components | Putative isochorismatase | ||||||
Keywords | HYDROLASE / CATALYTIC TRIAD / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY | ||||||
Function / homology | Isochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family / hydrolase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Putative isochorismatase hydrolase Function and homology information | ||||||
Biological species | Burkholderia xenovorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.22 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a putative isochorismatase (Bxe_A0706) from BURKHOLDERIA XENOVORANS LB400 at 1.22 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 | 3oqp.cif.gz | 190.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oqp.ent.gz | 156 KB | Display | PDB format |
PDBx/mmJSON format | 3oqp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3oqp_validation.pdf.gz | 444.7 KB | Display | wwPDB validaton report |
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Full document | 3oqp_full_validation.pdf.gz | 445.4 KB | Display | |
Data in XML | 3oqp_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 3oqp_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/3oqp ftp://data.pdbj.org/pub/pdb/validation_reports/oq/3oqp | 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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Details | ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. |
-Components
#1: Protein | Mass: 22569.668 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia xenovorans (bacteria) / Strain: LB400 / Gene: Bxeno_A3690, Bxe_A0706 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q13UL1 #2: Chemical | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | Sequence details | THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL 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: 1.9 Å3/Da / Density % sol: 35.27 % Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.9 | Details: 20.0% polyethylene glycol 3000, 0.15M sodium chloride, 0.1M HEPES pH 7.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97937,0.97898 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 10, 2010 / Details: Flat mirror (vertical focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.22→29.574 Å / Num. obs: 99282 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 10.39 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 9.46 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.22→29.574 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.972 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 1.965 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.042 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 5. PEG-200 (PG4) MOLECULES FROM THE CRYOPROTECTION SOLUTION ARE MODELED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 54.43 Å2 / Biso mean: 15.4416 Å2 / Biso min: 7.75 Å2
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Refinement step | Cycle: LAST / Resolution: 1.22→29.574 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.22→1.252 Å / Total num. of bins used: 20
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