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- PDB-7p7w: N-acetylglucosamine kinase from Plesiomonas shigelloides compexed... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7p7w | ||||||
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Title | N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine and ADP | ||||||
![]() | Ubiquitin-like protein SMT3,N-acetyl-D-glucosamine kinase | ||||||
![]() | SUGAR BINDING PROTEIN / N-acetylglucosamine recycling / carbohydrate kinase / ROK kinase. | ||||||
Function / homology | ![]() N-acetylglucosamine kinase / N-acetylglucosamine kinase activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / N-acetylglucosamine metabolic process / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors ...N-acetylglucosamine kinase / N-acetylglucosamine kinase activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / N-acetylglucosamine metabolic process / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / peptidoglycan turnover / septin ring / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / ubiquitin-like protein ligase binding / protein sumoylation / condensed nuclear chromosome / PML body / protein tag activity / zinc ion binding / ATP binding / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Roy, S. / Isupov, M.N. / Harmer, N.J. / Ames, J.R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Spinning sugars in antigen biosynthesis: characterization of the Coxiella burnetii and Streptomyces griseus TDP-sugar epimerases Authors: Cross, A.R. / Roy, S. / Vivoli Vega, M. / Rejzek, M. / Nepogodiev, S.A. / Cliff, M. / Salmon, D. / Isupov, M.N. / Field, R.A. / Prior, J.L. / Harmer, N.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 | ![]() | 168.3 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.7 MB | Display | ![]() |
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Full document | ![]() | 3.7 MB | Display | |
Data in XML | ![]() | 33.1 KB | Display | |
Data in CIF | ![]() | 49.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7p7iC ![]() 7p9lC ![]() 7p9pC ![]() 7p9yC ![]() 7pa1C ![]() 4db3S C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: -1 - 301 / Label seq-ID: 114 - 416
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
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Components
-Protein / Sugars , 2 types, 4 molecules AAABBB![](data/chem/img/NDG.gif)
![](data/chem/img/NDG.gif)
#1: Protein | Mass: 45960.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SMT3, YDR510W, D9719.15, nagK, PLESHI_11010 / Production host: ![]() ![]() References: UniProt: Q12306, UniProt: R8APY9, N-acetylglucosamine kinase #5: Sugar | |
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-Non-polymers , 9 types, 662 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-IMD / #6: Chemical | ChemComp-ZN / #7: Chemical | ChemComp-EDO / #8: Chemical | ChemComp-PEG / | #9: Chemical | #10: Chemical | ChemComp-IPA / | #11: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.85 % |
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Crystal grow | Temperature: 291 K / Method: microbatch Details: 120 mM alcohols; ; 0.1 M imidazole/MES pH 6.5; 30% each glycerol and PEG 4K Condition A3 of Morpheus screen (Molecular dimensions). Crystal was soaked for 60 seconds in cryoprotectant containing 10 mM ADP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 12M / Detector: PIXEL / Date: May 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9159 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→99.68 Å / Num. obs: 128365 / % possible obs: 100 % / Redundancy: 9.9 % / CC1/2: 0.999 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.57→1.6 Å / Num. unique obs: 6335 / CC1/2: 0.291 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4DB3 Resolution: 1.57→99.68 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.19 / WRfactor Rwork: 0.165 / Average fsc free: 0.8756 / Average fsc work: 0.8834 / Cross valid method: FREE R-VALUE / ESU R: 0.072 / ESU R Free: 0.074 / Details: Hydrogens have not been used
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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: BABINET MODEL PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.979 Å2
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Refinement step | Cycle: LAST / Resolution: 1.57→99.68 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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