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- PDB-6bmc: The structure of a dimeric type II DAH7PS associated with pyocyan... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6bmc | ||||||
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Title | The structure of a dimeric type II DAH7PS associated with pyocyanin biosynthesis in Pseudomonas aeruginosa | ||||||
![]() | Phospho-2-dehydro-3-deoxyheptonate aldolase | ||||||
![]() | TRANSFERASE / DAH7PS / 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase / shikimate pathway / pyocyanin biosynthesis | ||||||
Function / homology | ![]() phenazine biosynthetic process / 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / aromatic amino acid family biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sterritt, O.W. / Jameson, G.B. / Parker, E.J. | ||||||
![]() | ![]() Title: Structural and functional characterisation of the entry point to pyocyanin biosynthesis inPseudomonas aeruginosadefines a new 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase subclass. Authors: Sterritt, O.W. / Lang, E.J.M. / Kessans, S.A. / Ryan, T.M. / Demeler, B. / Jameson, G.B. / Parker, E.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 155.8 KB | Display | ![]() |
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PDB format | ![]() | 120.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.2 KB | Display | ![]() |
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Full document | ![]() | 471.3 KB | Display | |
Data in XML | ![]() | 29.3 KB | Display | |
Data in CIF | ![]() | 39 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5uxmS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44389.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: phzC, aroH_3, AOY09_05716, CAZ10_37830, PAERUG_E15_London_28_01_14_08300 Plasmid: pET28a(+) / Production host: ![]() ![]() References: UniProt: G3XCJ9, 3-deoxy-7-phosphoheptulonate synthase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.36 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop Details: 0.1-0.4 M NaF, 1 mM CoCl2, 1 mM PE, 16-22 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95363 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→85.27 Å / Num. obs: 21959 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 73.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.064 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.7→2.83 Å / Redundancy: 10 % / Rmerge(I) obs: 2.619 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2879 / CC1/2: 0.461 / Rpim(I) all: 1.28 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5UXM Resolution: 2.7→85.27 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.908 / Cross valid method: THROUGHOUT / ESU R Free: 0.416 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 87.938 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→85.27 Å
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Refine LS restraints |
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