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- PDB-7p7w: N-acetylglucosamine kinase from Plesiomonas shigelloides compexed... -

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Basic information

Entry
Database: PDB / ID: 7p7w
TitleN-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine and ADP
ComponentsUbiquitin-like protein SMT3,N-acetyl-D-glucosamine kinase
KeywordsSUGAR 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) / SUMOylation of SUMOylation proteins / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation ...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) / SUMOylation of SUMOylation proteins / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring / SUMOylation of DNA damage response and repair proteins / SUMOylation of RNA binding proteins / peptidoglycan turnover / SUMOylation of DNA replication proteins / SUMOylation of chromatin organization proteins / ubiquitin-like protein ligase binding / protein sumoylation / condensed nuclear chromosome / protein tag activity / zinc ion binding / ATP binding / identical protein binding / nucleus
Similarity search - Function
: / N-acetyl-D-glucosamine kinase / ROK family signature. / ROK family / ROK family / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / ATPase, nucleotide binding domain / Ubiquitin homologues / Ubiquitin-like domain ...: / N-acetyl-D-glucosamine kinase / ROK family signature. / ROK family / ROK family / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / ATPase, nucleotide binding domain / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / IMIDAZOLE / ISOPROPYL ALCOHOL / : / 2-acetamido-2-deoxy-alpha-D-glucopyranose / DI(HYDROXYETHYL)ETHER / Ubiquitin-like protein SMT3 / N-acetyl-D-glucosamine kinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Plesiomonas shigelloides 302-73 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsRoy, S. / Isupov, M.N. / Harmer, N.J. / Ames, J.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N001591/1 United Kingdom
CitationJournal: 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
DepositionJul 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Ubiquitin-like protein SMT3,N-acetyl-D-glucosamine kinase
BBB: Ubiquitin-like protein SMT3,N-acetyl-D-glucosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,33138
Polymers91,9202
Non-polymers3,41136
Water11,313628
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12890 Å2
ΔGint-23 kcal/mol
Surface area22780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.100, 115.100, 120.304
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

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

Dom-IDAuth asym-IDLabel asym-ID
1AAAA
2BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein / Sugars , 2 types, 4 molecules AAABBB

#1: Protein Ubiquitin-like protein SMT3,N-acetyl-D-glucosamine kinase / GlcNAc kinase


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 ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE / N-Acetylglucosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 9 types, 662 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#10: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 628 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: May 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.57→1.6 Å / Num. unique obs: 6335 / CC1/2: 0.291 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
MoRDaphasing
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DB3

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
RfactorNum. reflection% reflection
Rfree0.2112 6471 5.044 %
Rwork0.1857 121822 -
all0.187 --
obs-128293 99.981 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 29.979 Å2
Baniso -1Baniso -2Baniso -3
1--0.198 Å2-0.099 Å2-0 Å2
2---0.198 Å2-0 Å2
3---0.644 Å2
Refinement stepCycle: LAST / Resolution: 1.57→99.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4648 0 207 628 5483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125322
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.6427250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8455713
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53321.303284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20815885
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4941543
X-RAY DIFFRACTIONr_chiral_restr0.0960.2685
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024052
X-RAY DIFFRACTIONr_nbd_refined0.2220.22818
X-RAY DIFFRACTIONr_nbtor_refined0.3120.23525
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2547
X-RAY DIFFRACTIONr_metal_ion_refined0.180.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2010.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1390.231
X-RAY DIFFRACTIONr_mcbond_it3.1735.0382558
X-RAY DIFFRACTIONr_mcangle_it3.8299.3453223
X-RAY DIFFRACTIONr_scbond_it5.016.1092764
X-RAY DIFFRACTIONr_scangle_it6.61110.8683974
X-RAY DIFFRACTIONr_lrange_it8.0752.08823571
X-RAY DIFFRACTIONr_ncsr_local_group_10.0990.059847
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.099220.05008
12BBBX-RAY DIFFRACTIONLocal ncs0.099220.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.57-1.6110.3444790.34189180.34194030.6590.66799.93620.345
1.611-1.6550.3234850.32786750.32791650.720.72699.94540.329
1.655-1.7030.3234020.3285100.3289160.7630.77699.95510.317
1.703-1.7550.3094330.29482780.29587140.8030.8299.96560.286
1.755-1.8130.3034050.26579650.26783710.8410.85799.98810.25
1.813-1.8760.2573920.23277350.23381290.8910.90299.97540.212
1.876-1.9470.2523840.20874810.2178650.9040.921000.188
1.947-2.0270.2113900.19372010.19475910.9350.9391000.173
2.027-2.1170.2193430.18469360.18672800.9370.94699.98630.168
2.117-2.220.2093450.17866170.1869620.9440.9521000.164
2.22-2.340.1863220.16962960.1766180.9550.9571000.155
2.34-2.4820.1832920.16159710.16262630.9560.961000.149
2.482-2.6530.1973600.16555500.16759100.9510.9561000.154
2.653-2.8660.2012860.16452340.16655200.9470.9561000.153
2.866-3.1390.2042590.16548080.16750680.9440.95499.98030.156
3.139-3.5090.2012550.16543670.16746220.9470.9571000.156
3.509-4.0510.1791990.15338990.15540980.9610.9681000.144
4.051-4.9590.1561960.1532990.1534950.970.9711000.138
4.959-7.0050.2321600.20325710.20527320.9470.94899.96340.191
7.005-99.680.251840.21315110.21515960.9390.94899.93730.192

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