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- PDB-6smf: THE CRYSTAL STRUCTURE OF TYPE II DEHYDROQUINASE FROM ZYMOMONAS MOBILIS -
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Open data
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Basic information
Entry | Database: PDB / ID: 6smf | ||||||
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Title | THE CRYSTAL STRUCTURE OF TYPE II DEHYDROQUINASE FROM ZYMOMONAS MOBILIS | ||||||
![]() | 3-dehydroquinate dehydratase | ||||||
![]() | BIOSYNTHETIC PROTEIN / SHIKIMATE PATHWAY DEHYDRATASE | ||||||
Function / homology | ![]() 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: Biomacromolecular charge chirality detected using chiral plasmonic nanostructures Authors: Rodier, M. / Keijzer, C. / Milner, J. / Karimullah, A. / Roszak, A.W. / Barron, L.D. / Gadegaard, N. / Lapthorn, A.J. / Kadodwala, M. #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 | ![]() | 241.4 KB | Display | ![]() |
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PDB format | ![]() | 196.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 505.1 KB | Display | ![]() |
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Full document | ![]() | 515.7 KB | Display | |
Data in XML | ![]() | 25.1 KB | Display | |
Data in CIF | ![]() | 33 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6smeC ![]() 3lwzS 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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 3 - 146 / Label seq-ID: 6 - 149
NCS ensembles :
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 16127.410 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 31821 / ZM4 / CP4 / Gene: aroD, aroQ, ZMO0737, ZMO1_ZMO0737 / Plasmid: pET28a+ / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 100 molecules ![](data/chem/img/FLC.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FLC / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.37 % / Description: Triangular plate |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 15% PEG 8000, 0.1 M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 6, 2019 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91589 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.343→66.9 Å / Num. obs: 24281 / % possible obs: 94 % / Redundancy: 5.3 % / Biso Wilson estimate: 74.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.022 / Rrim(I) all: 0.05 / Net I/av σ(I): 18.4 / Net I/σ(I): 18.4 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 5.5 %
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 3LWZ Resolution: 2.343→66.9 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.955 / SU B: 20.495 / SU ML: 0.212 / SU R Cruickshank DPI: 0.3938 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.394 / ESU R Free: 0.236 / SU Rfree Cruickshank DPI: 0.2358 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 190.28 Å2 / Biso mean: 82.799 Å2 / Biso min: 33.46 Å2
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Refinement step | Cycle: final / Resolution: 2.343→66.9 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.343→2.404 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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