[English] 日本語
Yorodumi
- PDB-7p9l: N-acetylglucosamine kinase from Plesiomonas shigelloides compexed... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p9l
TitleN-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine-6-phosphate
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) / 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 / septin ring / SUMOylation of DNA damage response and repair proteins / peptidoglycan turnover / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of DNA replication proteins / 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 / 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 domain profile. ...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 domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Chem-4QY / : / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / 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: 1.75 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 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)95,31843
Polymers91,9202
Non-polymers3,39841
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10040 Å2
ΔGint-53 kcal/mol
Surface area24800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.508, 114.508, 119.266
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:

Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 0 - 301 / Label seq-ID: 115 - 416

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AAAA
22BBBB

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

-
Components

-
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
#4: Sugar ChemComp-4QY / 2-acetamido-2-deoxy-6-O-phosphono-beta-D-glucopyranose / beta-N-acetylglucosamine-6-phosphate / N-acetyl-6-O-phosphono-beta-D-glucosamine / 2-acetamido-2-deoxy-6-O-phosphono-beta-D-glucose / 2-acetamido-2-deoxy-6-O-phosphono-D-glucose / 2-acetamido-2-deoxy-6-O-phosphono-glucose


Type: D-saccharide, beta linking / Mass: 301.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16NO9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-GlcpNAc6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 8 types, 392 molecules

#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 64.03 %
Crystal growTemperature: 291 K / Method: microbatch
Details: 90 mM halogens; 0.1 M Tris/bicine pH 8.5; 30% each PEG 550 MME and PEG 20K, condition B9 from Morpheus screen (Molecular Dimensions)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.75→99.17 Å / Num. obs: 90389 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Redundancy: 3.8 % / CC1/2: 0.998 / Net I/σ(I): 8.4
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 4505 / CC1/2: 0.194

-
Processing

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

4db3


Resolution: 1.75→76.252 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.904 / SU ML: 0.086 / Cross valid method: FREE R-VALUE / ESU R: 0.101 / ESU R Free: 0.1 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2226 4568 5.056 %
Rwork0.1929 85782 -
all0.194 --
obs-90350 99.02 %
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: 36.515 Å2
Baniso -1Baniso -2Baniso -3
1--0.012 Å2-0.006 Å2-0 Å2
2---0.012 Å2-0 Å2
3---0.038 Å2
Refinement stepCycle: LAST / Resolution: 1.75→76.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4646 0 200 353 5199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0125221
X-RAY DIFFRACTIONr_angle_refined_deg1.751.6517063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7245691
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83721.341276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.21415863
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7861542
X-RAY DIFFRACTIONr_chiral_restr0.1120.2665
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023929
X-RAY DIFFRACTIONr_nbd_refined0.2140.22525
X-RAY DIFFRACTIONr_nbtor_refined0.3180.23427
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2340
X-RAY DIFFRACTIONr_metal_ion_refined0.3450.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.230.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1110.227
X-RAY DIFFRACTIONr_mcbond_it6.2536.3712521
X-RAY DIFFRACTIONr_mcangle_it7.29911.7753168
X-RAY DIFFRACTIONr_scbond_it8.0597.6382698
X-RAY DIFFRACTIONr_scangle_it10.11113.5273852
X-RAY DIFFRACTIONr_lrange_it11.61664.05122076
X-RAY DIFFRACTIONr_ncsr_local_group_10.0930.059718
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.092960.05008
12BBBX-RAY DIFFRACTIONLocal ncs0.092960.05008
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
1.75-1.7950.3563250.33463750.33567010.6750.70299.98510.334
1.795-1.8450.3233170.31961840.31965050.7870.79499.93850.315
1.845-1.8980.313060.28960060.2963140.8250.84899.96830.281
1.898-1.9560.3122790.27258800.27461630.8540.87299.93510.258
1.956-2.0210.3093090.25956810.26160090.8620.88899.68380.243
2.021-2.0910.2642620.23754600.23957490.9070.91399.53030.221
2.091-2.170.253010.22152760.22356200.9220.93199.23490.202
2.17-2.2590.2352470.21250290.21353620.9370.9498.39610.192
2.259-2.3590.2252460.19648780.19751600.9410.9599.30230.173
2.359-2.4740.212280.18746750.18849290.9480.95499.47250.165
2.474-2.6080.2043000.16944220.17147300.9550.96499.83090.15
2.608-2.7660.2152160.17542040.17744300.9490.96299.77430.159
2.766-2.9570.2192180.18139960.18342280.9490.96299.66890.165
2.957-3.1930.2142280.18236730.18439240.9530.96199.41390.171
3.193-3.4970.2161850.17633750.17836110.9520.96698.58760.17
3.497-3.9090.2151690.16530220.16732810.9570.9797.25690.166
3.909-4.5120.1781420.15326520.15429150.9720.97595.84910.158
4.512-5.5210.1741440.15222140.15325130.9710.97593.83210.159
5.521-7.7870.206900.1817540.18119500.9560.96394.56410.185
7.787-76.2520.216560.18310240.18411470.9510.96294.15870.203

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more