+Open data
-Basic information
Entry | Database: PDB / ID: 1t8x | ||||||
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Title | r106g kdo8ps with pep and a5p | ||||||
Components | 2-dehydro-3-deoxyphosphooctonate aldolase | ||||||
Keywords | TRANSFERASE / beta-alpha-barrel / kdo / kdo8ps / pep / a5p / kdo8p | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.8 Å | ||||||
Authors | Gatti, D.L. | ||||||
Citation | Journal: To be Published Title: Effects of the Arg106==>Gly mutation on the catalytic and conformational cycle of Aquifex aeolicus KDO8P synthase. Authors: Xu, X. / Wang, J. / Kona, F. / Divvela, P. / Stemmler, T. / Gatti, D.L. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Crystallography & NMR system: A new software suite for macromolecular structure determination. Authors: Brunger, A.T. / Adams, P.D. / Clore, G.M. / Delano, W.L. / Gros, P. / Grosse-Kunstleve, R. / Jiang, J.-S. / Kuszewski, J. / Nilges, M. / Pannu, N.S. / Read, R.J. / Rice, L.M. / Simonson, T. / Warren, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t8x.cif.gz | 125.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t8x.ent.gz | 95.5 KB | Display | PDB format |
PDBx/mmJSON format | 1t8x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1t8x_validation.pdf.gz | 474.7 KB | Display | wwPDB validaton report |
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Full document | 1t8x_full_validation.pdf.gz | 482.1 KB | Display | |
Data in XML | 1t8x_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | 1t8x_validation.cif.gz | 38 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/1t8x ftp://data.pdbj.org/pub/pdb/validation_reports/t8/1t8x | HTTPS FTP |
-Related structure data
Related structure data | 1t96C 1t99C 1fwwS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29674.266 Da / Num. of mol.: 2 / Mutation: r106g Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: KDSA, AQ_085 / Plasmid: pet28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: O66496, 3-deoxy-8-phosphooctulonate synthase |
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-Non-polymers , 5 types, 444 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-A5P / | #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: 2.748 Å3/Da / Density % sol: 50.6 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: PEG, Na-acetate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Monochromator: confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.8→54.02 Å / Num. all: 62521 / Num. obs: 60408 / % possible obs: 96.6 % / Observed criterion σ(I): 1 / Redundancy: 9.12 % / Biso Wilson estimate: 23.7 Å2 / Limit h max: 39 / Limit h min: 0 / Limit k max: 39 / Limit k min: 0 / Limit l max: 82 / Limit l min: 0 / Observed criterion F max: 214863.05 / Observed criterion F min: 0.115 / Rsym value: 0.095 / Net I/σ(I): 4.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1FWW Resolution: 1.8→54.02 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 54.323 Å2 / ksol: 0.34221 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso max: 89.37 Å2 / Biso mean: 34.3 Å2 / Biso min: 13.33 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→54.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.88 Å / Rfactor Rfree error: 0.02
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