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Yorodumi- PDB-7p7w: N-acetylglucosamine kinase from Plesiomonas shigelloides compexed... -
+Open data
-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 | ||||||
Components | Ubiquitin-like protein SMT3,N-acetyl-D-glucosamine kinase | ||||||
Keywords | SUGAR BINDING PROTEIN / N-acetylglucosamine recycling / carbohydrate kinase / ROK kinase. | ||||||
Function / homology | Function and homology information N-acetylglucosamine kinase / N-acetylglucosamine kinase activity / N-acetylglucosamine metabolic process / 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 / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors ...N-acetylglucosamine kinase / N-acetylglucosamine kinase activity / N-acetylglucosamine metabolic process / 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 / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins / peptidoglycan turnover / SUMOylation of DNA replication proteins / 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 | Saccharomyces cerevisiae (brewer's yeast) Plesiomonas shigelloides 302-73 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | Roy, S. / Isupov, M.N. / Harmer, N.J. / Ames, J.R. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p7w.cif.gz | 168.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p7w.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7p7w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p7/7p7w ftp://data.pdbj.org/pub/pdb/validation_reports/p7/7p7w | HTTPS FTP |
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-Related structure data
Related structure data | 7p7iC 7p9lC 7p9pC 7p9yC 7pa1C 4db3S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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) |
-Components
-Protein / Sugars , 2 types, 4 molecules AAABBB
#1: Protein | Mass: 45960.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) Plesiomonas shigelloides 302-73 (bacteria) Strain: ATCC 204508 / S288c / Gene: SMT3, YDR510W, D9719.15, nagK, PLESHI_11010 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q12306, UniProt: R8APY9, N-acetylglucosamine kinase #5: Sugar | |
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-Non-polymers , 9 types, 662 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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