+Open data
-Basic information
Entry | Database: PDB / ID: 1fxp | ||||||
---|---|---|---|---|---|---|---|
Title | AQUIFEX AEOLICUS KDO8P SYNTHASE IN COMPLEX WITH CADMIUM | ||||||
Components | 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE | ||||||
Keywords | LYASE / kdo8ps / kdo8p / kdo / PEP / A5P / beta/alpha barrel | ||||||
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 / Resolution: 1.8 Å | ||||||
Authors | Duewel, H.S. / Radaev, S. / Wang, J. / Woodard, R.W. / Gatti, D.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Substrate and metal complexes of 3-deoxy-D-manno-octulosonate-8-phosphate synthase from Aquifex aeolicus at 1.9-A resolution. Implications for the condensation mechanism. Authors: Duewel, H.S. / Radaev, S. / Wang, J. / Woodard, R.W. / Gatti, D.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1fxp.cif.gz | 113.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1fxp.ent.gz | 88.2 KB | Display | PDB format |
PDBx/mmJSON format | 1fxp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/1fxp ftp://data.pdbj.org/pub/pdb/validation_reports/fx/1fxp | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
| ||||||||||
Details | The biological assembly is a tetramer constructed from chain A and chain B and their symmetry partners generated by application of the symmetry operation (x=y, y=x, z=-z) |
-Components
#1: Protein | Mass: 29774.406 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Plasmid: PAAKDSA / Production host: Escherichia coli (E. coli) / References: UniProt: O66496, EC: 4.1.2.16 #2: Chemical | ChemComp-PO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.72 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 100 mM Na-acetate, 6% PEG 4000, pH 4.8, VAPOR DIFFUSION, HANGING DROP at 278K Na-acetate, 6% PEG 4000 , temperature 278.0K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃Details: drop contains protein and reservoir solution in a 1:1 ratio | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jun 4, 2000 |
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→26.2 Å / Num. all: 52273 / Num. obs: 52273 / % possible obs: 83.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 35.3 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 2.95 % / Rmerge(I) obs: 0.578 / Num. unique all: 3522 / % possible all: 34.4 |
Reflection | *PLUS Lowest resolution: 26 Å / Num. obs: 54713 / Num. measured all: 475864 |
Reflection shell | *PLUS % possible obs: 34.4 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.8→26.2 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 93184.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.89 Å2 / ksol: 0.377 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.2 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→26.2 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 41.6 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|