+Open data
-Basic information
Entry | Database: PDB / ID: 1fy6 | ||||||
---|---|---|---|---|---|---|---|
Title | AQUIFEX AEOLICUS KDO8P SYNTHASE IN COMPLEX WITH CADMIUM AND A5P | ||||||
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: 1.89 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 | 1fy6.cif.gz | 118.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1fy6.ent.gz | 91.8 KB | Display | PDB format |
PDBx/mmJSON format | 1fy6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fy6_validation.pdf.gz | 464.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1fy6_full_validation.pdf.gz | 473.5 KB | Display | |
Data in XML | 1fy6_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 1fy6_validation.cif.gz | 34.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/1fy6 ftp://data.pdbj.org/pub/pdb/validation_reports/fy/1fy6 | 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 | #3: Chemical | #4: Chemical | ChemComp-A5P / | #5: 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: 55.75 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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, 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: SIEMENS HI-STAR / Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→43.14 Å / Num. all: 45480 / Num. obs: 45480 / % possible obs: 84.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 11.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 29.2 |
Reflection shell | Resolution: 1.89→2.01 Å / Redundancy: 2.43 % / Rmerge(I) obs: 0.258 / Num. unique all: 5850 / % possible all: 65.9 |
Reflection | *PLUS Lowest resolution: 43 Å / Num. measured all: 381111 |
Reflection shell | *PLUS % possible obs: 65.9 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.89→43.14 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 11218917.4 / 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: 50.22 Å2 / ksol: 0.378 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.7 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→43.14 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.89→2.01 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 43 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|