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Yorodumi- PDB-2nwr: Crystal structure of C11N mutant of KDO8P Synthase in complex with PEP -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nwr | ||||||
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Title | Crystal structure of C11N mutant of KDO8P Synthase in complex with PEP | ||||||
Components | 2-dehydro-3-deoxyphosphooctonate aldolase | ||||||
Keywords | TRANSFERASE / KDO / KDO8P / KDO8PS / PEP / A5P | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 | 2nwr.cif.gz | 122.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nwr.ent.gz | 93.9 KB | Display | PDB format |
PDBx/mmJSON format | 2nwr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/2nwr ftp://data.pdbj.org/pub/pdb/validation_reports/nw/2nwr | HTTPS FTP |
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-Related structure data
Related structure data | 2ef9C 2nwsC 2nx1C 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
#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: Chemical | #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: 2.75 Å3/Da / Density % sol: 55.29 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1 Å |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→36 Å / Num. all: 105825 / Num. obs: 103074 / % possible obs: 97.4 % / Observed criterion σ(I): 2.2 / Redundancy: 5.5 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 3.9 |
-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: 1.5→35.63 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 449237.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.613 Å2 / ksol: 0.337005 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→35.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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