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- PDB-7p7i: Native structure of N-acetylglucosamine kinase from Plesiomonas s... -

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Basic information

Entry
Database: PDB / ID: 7p7i
TitleNative structure of N-acetylglucosamine kinase from Plesiomonas shigelloides
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 / SUMOylation of transcription cofactors / 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) / SUMO is proteolytically processed / SUMOylation of transcription factors / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation / 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 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: 1.7 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 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 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.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 15, 2023Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Dec 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 1.4Feb 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)93,32419
Polymers91,9202
Non-polymers1,40417
Water9,242513
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7700 Å2
ΔGint-1 kcal/mol
Surface area24040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.230, 95.230, 180.550
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

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

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

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Components

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Protein , 1 types, 2 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

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Non-polymers , 7 types, 530 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: 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
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 513 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.57 Å3/Da / Density % sol: 52.16 %
Crystal growTemperature: 291 K / Method: microbatch
Details: 60 mM divalent cations; 0.1 M Tris/bicine pH 8.5; 12.5% each MPD, PEG 1K, PEG 3350. condition A12 from Morpheus screen (Molecular Dimensions)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→75.01 Å / Num. obs: 104319 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / CC1/2: 0.999 / Net I/σ(I): 13.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.1 % / Num. unique obs: 5073 / CC1/2: 0.27 / % possible all: 99.7

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Processing

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

4db3


Resolution: 1.7→60.888 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 3.25 / SU ML: 0.09 / Cross valid method: FREE R-VALUE / ESU R: 0.084 / ESU R Free: 0.086 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2103 5218 5.006 %
Rwork0.1827 99021 -
all0.184 --
obs-104239 99.517 %
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: 43.654 Å2
Baniso -1Baniso -2Baniso -3
1-1.128 Å20.564 Å20 Å2
2--1.128 Å20 Å2
3----3.66 Å2
Refinement stepCycle: LAST / Resolution: 1.7→60.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4639 0 84 513 5236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0125105
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.6366938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6635692
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.22321.825274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67915873
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4931539
X-RAY DIFFRACTIONr_chiral_restr0.1140.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023915
X-RAY DIFFRACTIONr_nbd_refined0.2050.22457
X-RAY DIFFRACTIONr_nbtor_refined0.3140.23485
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2415
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2050.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1380.214
X-RAY DIFFRACTIONr_mcbond_it4.7847.9172525
X-RAY DIFFRACTIONr_mcangle_it5.28414.6743174
X-RAY DIFFRACTIONr_scbond_it7.3078.9732580
X-RAY DIFFRACTIONr_scangle_it8.74216.0593719
X-RAY DIFFRACTIONr_lrange_it9.04478.42421633
X-RAY DIFFRACTIONr_ncsr_local_group_10.0940.059784
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.093950.05008
12BBBX-RAY DIFFRACTIONLocal ncs0.093950.05008
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
1.7-1.7440.4263740.42871920.42876080.4470.45799.44790.415
1.744-1.7920.3813880.38870730.38774990.5380.52499.49330.371
1.792-1.8440.3724170.35867990.35972500.6490.64499.5310.338
1.844-1.90.333470.31767050.31870750.7220.72999.67490.288
1.9-1.9630.3163200.28864910.2968340.7920.80799.66350.254
1.963-2.0320.2823090.25362940.25566440.8680.87899.38290.217
2.032-2.1080.2623000.23260820.23364110.8930.90899.54770.199
2.108-2.1940.2442540.21158950.21261650.920.93299.74050.179
2.194-2.2920.2473430.19655590.19959210.9280.94399.67910.164
2.292-2.4030.2232750.1953610.19156570.9420.95199.62880.164
2.403-2.5330.2192830.19350890.19553870.9490.95399.72150.165
2.533-2.6860.2172530.17948550.18151530.9540.96399.12670.158
2.686-2.8710.2092040.17446080.17548350.9570.96699.52430.157
2.871-3.1010.2122520.17442500.17745170.9580.96699.66790.163
3.101-3.3960.2291950.16839590.17141650.9570.96999.73590.161
3.396-3.7950.1952040.15635560.15837740.9650.97599.6290.151
3.795-4.380.1491570.1331700.13133450.9790.98399.46190.127
4.38-5.3570.1341610.12127030.12228830.9840.98599.3410.122
5.357-7.5470.1881100.15621390.15822740.9690.97698.90060.155
7.547-60.8880.184720.18512400.18513440.970.96797.6190.197

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