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Yorodumi- PDB-3r2e: Dihydroneopterin aldolase/dihydroneopterin triphosphate 2'-epimer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3r2e | ||||||
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Title | Dihydroneopterin aldolase/dihydroneopterin triphosphate 2'-epimerase from Yersinia pestis. | ||||||
Components | Dihydroneopterin aldolase | ||||||
Keywords | LYASE / structural genomics / IDP90567 / Center for Structural Genomics of Infectious Diseases / CSGID / bifunctional / dihydroneopterin aldolase / dihydroneopterin triphosphate 2'-epimerase | ||||||
Function / homology | Function and homology information dihydroneopterin aldolase / dihydroneopterin aldolase activity / folic acid-containing compound metabolic process / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Yersinia pestis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Osipiuk, J. / Maltseva, N. / Makowska-Grzyska, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: Dihydroneopterin aldolase/dihydroneopterin triphosphate 2'-epimerase from Yersinia pestis Authors: Osipiuk, J. / Maltseva, N. / Makowska-Grzyska, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r2e.cif.gz | 62.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r2e.ent.gz | 45.4 KB | Display | PDB format |
PDBx/mmJSON format | 3r2e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3r2e_validation.pdf.gz | 426.2 KB | Display | wwPDB validaton report |
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Full document | 3r2e_full_validation.pdf.gz | 428.6 KB | Display | |
Data in XML | 3r2e_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | 3r2e_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r2/3r2e ftp://data.pdbj.org/pub/pdb/validation_reports/r2/3r2e | HTTPS FTP |
-Related structure data
Related structure data | 2o90S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16149.166 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO-92 / Gene: folB, YPO0648 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q0WJ22, UniProt: A0A5P8YJX5*PLUS, dihydroneopterin aldolase |
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#2: 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: 2.14 Å3/Da / Density % sol: 42.59 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M calcium chloride, 0.1 M Bis-tris buffer, 45% MPD, 10 mM guanine, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 24, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.15→31 Å / Num. all: 7990 / Num. obs: 7990 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 57.7 Å2 / Rmerge(I) obs: 0.06 / Χ2: 1.595 / Net I/σ(I): 12.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2O90 Resolution: 2.15→31 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 16.998 / SU ML: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
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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 max: 157.66 Å2 / Biso mean: 67.9161 Å2 / Biso min: 33.68 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.201 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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