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- PDB-6ojo: Dihydroneopterin aldolase (DHNA) from Yersinia pestis co-crystall... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ojo | ||||||
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Title | Dihydroneopterin aldolase (DHNA) from Yersinia pestis co-crystallized with pterine | ||||||
![]() | 7,8-dihydroneopterin aldolase | ||||||
![]() | BIOSYNTHETIC PROTEIN / folB folate pathway | ||||||
Function / homology | ![]() dihydroneopterin aldolase / dihydroneopterin aldolase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / kinase activity / phosphorylation / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Bourne, C.R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Dihydroneopterin aldolase (DHNA) from Yersinia pestis co-crystallized with pterine Authors: Bourne, C.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.8 KB | Display | ![]() |
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PDB format | ![]() | 89.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 277.9 KB | Display | ![]() |
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Full document | ![]() | 280.8 KB | Display | |
Data in XML | ![]() | 2 KB | Display | |
Data in CIF | ![]() | 9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3r2eS S: Starting model for refinement |
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Similar structure data |
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Links
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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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Components
#1: Protein | Mass: 16149.166 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q8CZR7, UniProt: A0A5P8YJX5*PLUS, dihydroneopterin aldolase #2: Chemical | ChemComp-PE0 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.22 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, sitting drop Details: 0.1 M BisTris pH 6.5 0.2 M CaCl2 0.05 M NaCl 47% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.886→41.557 Å / Num. obs: 45556 / % possible obs: 99 % / Redundancy: 4.2 % / Biso Wilson estimate: 19.45 Å2 / Rrim(I) all: 0.11 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.886→1.954 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4210 / Rrim(I) all: 0.584 / % possible all: 91.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3r2e Resolution: 1.886→41.557 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.27
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.29 Å2 / Biso mean: 22.2082 Å2 / Biso min: 8.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.886→41.557 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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