[English] 日本語
Yorodumi- PDB-1lrn: Aquifex aeolicus KDO8P synthase H185G mutant in complex with Cadmium -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lrn | ||||||
---|---|---|---|---|---|---|---|
Title | Aquifex aeolicus KDO8P synthase H185G mutant in complex with Cadmium | ||||||
Components | KDO-8-phosphate synthetase | ||||||
Keywords | LYASE / Kdo8ps / kdo8p / kdo | ||||||
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: 2.1 Å | ||||||
Authors | Wang, J. / Duewel, H.S. / Stuckey, J.A. / Woodard, R.W. / Gatti, D.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Function of His185 in Aquifex aeolicus 3-Deoxy-D-manno-octulosonate 8-Phosphate Synthase Authors: Wang, J. / Duewel, H.S. / Stuckey, J.A. / Woodard, R.W. / Gatti, D.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1lrn.cif.gz | 116.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1lrn.ent.gz | 89.9 KB | Display | PDB format |
PDBx/mmJSON format | 1lrn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/1lrn ftp://data.pdbj.org/pub/pdb/validation_reports/lr/1lrn | 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 b application of the symmetry operation (x=y, y=x, z=-z) |
-Components
#1: Protein | Mass: 29693.312 Da / Num. of mol.: 2 / Mutation: H185G 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: 2.76 Å3/Da / Density % sol: 55.5 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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, temperature 278K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Details: Duewel, H.S., (2001) J.Biol.Chem., 276, 8393. | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Apr 16, 2002 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→24 Å / Num. obs: 37881 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.1→2.23 Å / % possible all: 90.5 |
Reflection | *PLUS Lowest resolution: 24 Å / Redundancy: 8 % / Num. measured all: 304220 / Rmerge(I) obs: 0.166 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→24 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.7626 Å2 / ksol: 0.362865 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.5 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→24 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 24 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.203 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|