+Open data
-Basic information
Entry | Database: PDB / ID: 1x6u | |||||||||
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Title | KDO8P synthase in it's binary complex with the product KDO8P | |||||||||
Components | 2-dehydro-3-deoxyphosphooctonate aldolase | |||||||||
Keywords | TRANSFERASE / KDO8P | |||||||||
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 | 1x6u.cif.gz | 66.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x6u.ent.gz | 48.8 KB | Display | PDB format |
PDBx/mmJSON format | 1x6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1x6u_validation.pdf.gz | 837.2 KB | Display | wwPDB validaton report |
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Full document | 1x6u_full_validation.pdf.gz | 850.1 KB | Display | |
Data in XML | 1x6u_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 1x6u_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x6/1x6u ftp://data.pdbj.org/pub/pdb/validation_reports/x6/1x6u | HTTPS FTP |
-Related structure data
Related structure data | 1phwSC 1q3nC 1x8fC 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 | The biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operations: X,Y,Z -X,-Y,Z -X,Y,-Z X,-Y,-Z Z,X,Y Z,-X,-Y -Z,-X,Y -Z,X,-Y Y,Z,X -Y,Z,-X Y,-Z,-X -Y,-Z,X 1/2+X,1/2+Y,1/2+Z 1/2-X,1/2-Y,1/2+Z 1/2-X,1/2+Y,1/2-Z 1/2+X,1/2-Y,1/2-Z 1/2+Z,1/2+X,1/2+Y 1/2+Z,1/2-X,1/2-Y 1/2-Z,1/2-X,1/2+Y 1/2-Z,1/2+X,1/2-Y 1/2+Y,1/2+Z,1/2+X 1/2-Y,1/2+Z,1/2-X 1/2+Y,1/2-Z,1/2-X 1/2-Y,1/2-Z,1/2+X |
-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 / Plasmid: pJU1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha References: UniProt: P0A715, 3-deoxy-8-phosphooctulonate synthase |
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#2: Sugar | ChemComp-DO8 / |
#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: 2.2 Å3/Da / Density % sol: 42.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: PEG4000, Glycerol, 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: 0.934 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 28, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. obs: 6950 / % possible obs: 90.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.2 % / Rsym value: 0.075 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 7 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 5.3 / Num. unique all: 768 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PHW Resolution: 2.7→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 66.35 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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