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Yorodumi- PDB-2nx1: Structural and mechanistic changes along an engineered path from ... -
+Open data
-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 | |||||||||
Components | 2-dehydro-3-deoxyphosphooctonate aldolase | |||||||||
Keywords | TRANSFERASE / KDO / KDO8P / KDO8PS / PEP / A5P / RP5 | |||||||||
Function / homology | Function and homology information 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 | Aquifex aeolicus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Kona, F. / Xu, X. / Martin, P. / Kuzmic, P. / Gatti, D.L. | |||||||||
Citation | Journal: Biochemistry / Year: 2007 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nx1.cif.gz | 128.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nx1.ent.gz | 98.5 KB | Display | PDB format |
PDBx/mmJSON format | 2nx1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nx1_validation.pdf.gz | 472.5 KB | Display | wwPDB validaton report |
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Full document | 2nx1_full_validation.pdf.gz | 481.2 KB | Display | |
Data in XML | 2nx1_validation.xml.gz | 28.3 KB | Display | |
Data in CIF | 2nx1_validation.cif.gz | 41.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/2nx1 ftp://data.pdbj.org/pub/pdb/validation_reports/nx/2nx1 | 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 (ref.) |
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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 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.) Aquifex aeolicus (bacteria) / Gene: kdsA / Production host: Escherichia coli (E. coli) 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: X-RAY DIFFRACTION |
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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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
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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 |
-Processing
Software | Name: CNS / Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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