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- PDB-2nx3: Structural and mechanistic changes along an engineered path from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2nx3 | ||||||
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Title | Structural and mechanistic changes along an engineered path from metallo to non-metallo KDO8P synthase | ||||||
![]() | 2-dehydro-3-deoxyphosphooctonate aldolase | ||||||
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Function / homology | ![]() monosaccharide biosynthetic process / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kona, F. / Xu, X. / Martin, P. / Kuzmic, P. / Gatti, D.L. | ||||||
![]() | ![]() Title: Structural and Mechanistic Changes along an Engineered Path from Metallo to Nonmetallo 3-Deoxy-d-manno-octulosonate 8-Phosphate Synthases. Authors: Kona, F. / Xu, X. / Martin, P. / Kuzmic, P. / Gatti, D.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 645 KB | Display | ![]() |
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PDB format | ![]() | 531.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2ef9C ![]() 2nwrC ![]() 2nwsC ![]() 2nx1C ![]() 2nxgC ![]() 2nxhC ![]() 2nxiC ![]() 1fwnS ![]() 2nxk S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29738.355 Da / Num. of mol.: 12 / Mutation: C11N, S235P, Q237A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: O66496, ![]() #2: Chemical | ChemComp-PEP / ![]() #3: Chemical | ChemComp-A5P / #4: Chemical | ChemComp-1NT / ( | #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.85 % |
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-Data collection
Diffraction source | Source: ![]() |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→29.8 Å / Num. all: 217079 / Num. obs: 206008 / % possible obs: 0.949 % / Observed criterion σ(I): 2.3 / Redundancy: 6.6 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 6.9 |
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Processing
Software | Name: CNS / Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure![]() ![]() Starting model: PDB Entry 1FWN Resolution: 2.1→29.79 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 760463.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.6023 Å2 / ksol: 0.345114 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→29.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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Xplor file |
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