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- PDB-1q3n: Crystal structure of KDO8P synthase in its binary complex with su... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1q3n | ||||||
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Title | Crystal structure of KDO8P synthase in its binary complex with substrate PEP | ||||||
![]() | 2-dehydro-3-deoxyphosphooctonate aldolase | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vainer, R. / Belakhov, V. / Rabkin, E. / Baasov, T. / Adir, N. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.2 KB | Display | ![]() |
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PDB format | ![]() | 50 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | 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 ( |
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Similar structure data |
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Links
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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; |
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Components
#1: Protein | Mass: 30870.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: P0A715, ![]() |
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#2: Chemical | ChemComp-PEP / ![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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![]() |
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 |
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Processing
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Refinement | Method to determine structure![]() ![]() 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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