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Yorodumi- PDB-1fwt: AQUIFEX AEOLICUS KDO8P SYNTHASE IN COMPLEX WITH PEP, E4P AND CADMIUM -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fwt | ||||||
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Title | AQUIFEX AEOLICUS KDO8P SYNTHASE IN COMPLEX WITH PEP, E4P AND 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: 1.9 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fwt.cif.gz | 118.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fwt.ent.gz | 91.2 KB | Display | PDB format |
PDBx/mmJSON format | 1fwt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/1fwt ftp://data.pdbj.org/pub/pdb/validation_reports/fw/1fwt | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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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
-Protein / Sugars , 2 types, 3 molecules AB
#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 #4: Sugar | ChemComp-E4P / | |
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-Non-polymers , 4 types, 228 molecules
#2: Chemical | #3: Chemical | #5: Chemical | ChemComp-PO4 / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.14 % | ||||||||||||||||||||
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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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25.45 Å / Num. all: 46313 / Num. obs: 46313 / % possible obs: 88.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.9→2.02 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.62 / Num. unique all: 4675 / % possible all: 54.5 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 556519 |
Reflection shell | *PLUS % possible obs: 54.5 % |
-Processing
Software |
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Refinement | Resolution: 1.9→25.45 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 700617 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.13 Å2 / ksol: 0.351 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→25.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 34.2 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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