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Yorodumi- PDB-2y5j: Crystal structure of Burkholderia cenocepacia dihydropteroate syn... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y5j | ||||||
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Title | Crystal structure of Burkholderia cenocepacia dihydropteroate synthase. | ||||||
Components | DIHYDROPTEROATE SYNTHASE | ||||||
Keywords | TRANSFERASE / FOLATE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | BURKHOLDERIA CENOCEPACIA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | ||||||
Authors | Morgan, R.E. / Batot, G.O. / Dement, J.M. / Rao, V.A. / Eadsforth, T.C. / Hunter, W.N. | ||||||
Citation | Journal: Bmc Struct.Biol. / Year: 2011 Title: Crystal Structures of Burkholderia Cenocepacia Dihydropteroate Synthase in the Apo-Form and Complexed with the Product 7,8-Dihydropteroate. Authors: Morgan, R.E. / Batot, G.O. / Dement, J.M. / Rao, V.A. / Eadsforth, T.C. / Hunter, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y5j.cif.gz | 66.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y5j.ent.gz | 48.3 KB | Display | PDB format |
PDBx/mmJSON format | 2y5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y5/2y5j ftp://data.pdbj.org/pub/pdb/validation_reports/y5/2y5j | HTTPS FTP |
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-Related structure data
Related structure data | 2y5sC 1aj2S C: citing same article (ref.) S: Starting model for refinement |
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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: 31002.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BURKHOLDERIA CENOCEPACIA (bacteria) / Strain: LMG 16656 Description: BELGIAN CO-ORDINATED COLLECTIONS OF MICRO-ORGANISMS, BACTERIA COLLECTION (BCCM/LMG) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4E5F5, dihydropteroate synthase | ||
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#2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 7.8 Details: RESERVOIR CONDITIONS 0.3 M TRIS/HCL PH8, 10% PEG 8000. PROTEIN SOLUTION BCDHPS AT 7.5 MGML-1, 2MM SULPHADOXINE, 50MM TRIS/HCL PH7.5, 250 MM NACL., pH 7.8 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: RIGAKU CCD / Detector: CCD / Date: Aug 6, 2009 / Details: MIRRORS |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→57.28 Å / Num. obs: 12564 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 47.7 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.4 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AJ2 Resolution: 2.33→56.99 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.903 / SU B: 7.975 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.392 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.36 Å2
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Refinement step | Cycle: LAST / Resolution: 2.33→56.99 Å
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Refine LS restraints |
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