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Yorodumi- PDB-1q3n: Crystal structure of KDO8P synthase in its binary complex with su... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q3n | ||||||
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Title | Crystal structure of KDO8P synthase in its binary complex with substrate PEP | ||||||
Components | 2-dehydro-3-deoxyphosphooctonate aldolase | ||||||
Keywords | TRANSFERASE / BETA-ALPHA-BARRELS / LYASE / LIPOPOLYSACCHARIDE / Phosphoenolpyruvate | ||||||
Function / homology | Function and homology information 3-deoxy-8-phosphooctulonate synthase / 3-deoxy-8-phosphooctulonate synthase activity / keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / protein-containing complex / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Vainer, R. / Belakhov, V. / Rabkin, E. / Baasov, T. / Adir, N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Crystal structures of Escherichia coli KDO8P synthase complexes reveal the source of catalytic irreversibility. Authors: Vainer, R. / Belakhov, V. / Rabkin, E. / Baasov, T. / Adir, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q3n.cif.gz | 67.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q3n.ent.gz | 50 KB | Display | PDB format |
PDBx/mmJSON format | 1q3n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/1q3n ftp://data.pdbj.org/pub/pdb/validation_reports/q3/1q3n | HTTPS FTP |
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-Related structure data
Related structure data | 1phwC 1x6uC 1x8fC 1d9eS 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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Details | THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. The biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations: x,y,z; -x,-y,z; -x,y,-z; x,y,-z; |
-Components
#1: Protein | Mass: 30870.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: KDSA / Production host: Escherichia coli (E. coli) References: UniProt: P0A715, 3-deoxy-8-phosphooctulonate synthase |
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#2: Chemical | ChemComp-PEP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: PEG 4000, Glycrol, Tris-HCl , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 23, 2003 |
Radiation | Monochromator: Bent mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→100 Å / Num. obs: 8169 / % possible obs: 96.3 % / Redundancy: 6 % / Rmerge(I) obs: 0.06 / Rsym value: 0.074 |
Reflection shell | Resolution: 2.62→2.68 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.396 / Num. unique all: 526 / Rsym value: 0.074 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1D9E Resolution: 2.7→24 Å / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.7→24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.8 Å /
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