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- PDB-6hsq: The crystal structure of type II Dehydroquinase from Psychromonas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6hsq | ||||||
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Title | The crystal structure of type II Dehydroquinase from Psychromonas ingrahamii 37 crystal form 1 | ||||||
![]() | 3-dehydroquinate dehydratase | ||||||
![]() | BIOSYNTHETIC PROTEIN / shikimate pathway / dehydratase | ||||||
Function / homology | ![]() quinate catabolic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Lapthorn, A.J. / Roszak, A.W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The crystal structure of type II Dehydroquinase from Butyrivibrio crossotus DSM 2876 Authors: Lapthorn, A.J. / Koyroytsaltis-McQuire, D. / Roszak, A.W. #1: Journal: AMB Express / Year: 2015 Title: Unraveling the kinetic diversity of microbial 3-dehydroquinate dehydratases of shikimate pathway. Authors: Liu, C. / Liu, Y.M. / Sun, Q.L. / Jiang, C.Y. / Liu, S.J. #2: ![]() Title: The structure and mechanism of the type II dehydroquinase from Streptomyces coelicolor. Authors: Roszak, A.W. / Robinson, D.A. / Krell, T. / Hunter, I.S. / Fredrickson, M. / Abell, C. / Coggins, J.R. / Lapthorn, A.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 | ![]() | 252.5 KB | Display | ![]() |
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PDB format | ![]() | 205.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6hs8C ![]() 6hs9C ![]() 6hsaC ![]() 6hsbC ![]() 4rc9S 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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Components on special symmetry positions |
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Components
#1: Protein | Mass: 16803.170 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 37 / Gene: aroQ, Ping_3121 / Plasmid: pET28a+ / Production host: ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.37 % / Description: pyramidal |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1M Lithium Sulphate, 0.1M MOPS pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 12, 2018 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.456→98.561 Å / Num. obs: 150335 / % possible obs: 95.9 % / Redundancy: 9.9 % / Biso Wilson estimate: 22.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.028 / Rrim(I) all: 0.12 / Net I/σ(I): 14.6 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 9.4 %
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 0.42 / Cor.coef. Fo:Fc: 0.447 / Cor.coef. Io to Ic: 0.481
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4RC9 Resolution: 1.46→98.56 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.791 / SU ML: 0.034 / SU R Cruickshank DPI: 0.0532 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.054 Details: U VALUES : WITH TLS ADDED 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.11 Å2 / Biso mean: 25.658 Å2 / Biso min: 13.51 Å2
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Refinement step | Cycle: final / Resolution: 1.46→98.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.456→1.494 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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