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- PDB-2nx1: 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: 2nx1 | |||||||||
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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 | |||||||||
![]() | TRANSFERASE / KDO / KDO8P / KDO8PS / PEP / A5P / RP5 | |||||||||
Function / homology | ![]() monosaccharide biosynthetic process / 3-deoxy-8-phosphooctulonate synthase / 3-deoxy-8-phosphooctulonate synthase activity / keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / cytosol 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 | ![]() | 128.5 KB | Display | ![]() |
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PDB format | ![]() | 98.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 472.5 KB | Display | ![]() |
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Full document | ![]() | 481.2 KB | Display | |
Data in XML | ![]() | 28.3 KB | Display | |
Data in CIF | ![]() | 41.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ef9C ![]() 2nwrC ![]() 2nwsC ![]() 2nx3C ![]() 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 29785.367 Da / Num. of mol.: 2 / Mutation: C11N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O66496, 3-deoxy-8-phosphooctulonate synthase #2: Sugar | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.98 % |
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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: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→37 Å / Num. all: 64012 / Num. obs: 56843 / % possible obs: 88.8 % / Observed criterion σ(I): 2.1 / Redundancy: 9.1 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 4.1 |
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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: 1.8→36.71 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 317490.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 4.4
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.7729 Å2 / ksol: 0.314475 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→36.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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