[English] 日本語
Yorodumi
- PDB-6q27: N-acetylmannosamine kinase with N-acetylmannosamine from Staphylo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6q27
TitleN-acetylmannosamine kinase with N-acetylmannosamine from Staphylococcus aureus
ComponentsGlucokinase
KeywordsTRANSFERASE / ROK / Sugar Kinase
Function / homology
Function and homology information


beta-glucoside kinase / beta-glucoside kinase activity / glucokinase / glucokinase activity
Similarity search - Function
ROK family / ROK family / ATPase, nucleotide binding domain
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-mannopyranose / Glucokinase / ROK family protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCoombes, D. / Horne, C.R. / Davies, J.S. / Dobson, R.C.J.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: The basis for non-canonical ROK family function in theN-acetylmannosamine kinase from the pathogenStaphylococcus aureus.
Authors: Coombes, D. / Davies, J.S. / Newton-Vesty, M.C. / Horne, C.R. / Setty, T.G. / Subramanian, R. / Moir, J.W.B. / Friemann, R. / Panjikar, S. / Griffin, M.D.W. / North, R.A. / Dobson, R.C.J.
History
DepositionAug 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 18, 2020Group: Data collection / Database references / Category: chem_comp / citation
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glucokinase
B: Glucokinase
C: Glucokinase
D: Glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,2248
Polymers126,3394
Non-polymers8854
Water1,60389
1
A: Glucokinase
B: Glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6124
Polymers63,1702
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-1 kcal/mol
Surface area23290 Å2
MethodPISA
2
C: Glucokinase
hetero molecules

D: Glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6124
Polymers63,1702
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area4270 Å2
ΔGint-2 kcal/mol
Surface area23290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.236, 101.353, 133.222
Angle α, β, γ (deg.)90.000, 90.150, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 53 or resid 55...
21(chain B and (resid 2 through 53 or resid 55...
31(chain C and (resid 2 through 53 or resid 55...
41(chain D and (resid 2 through 53 or resid 55...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 53 or resid 55...A2 - 53
121(chain A and (resid 2 through 53 or resid 55...A55
131(chain A and (resid 2 through 53 or resid 55...A57 - 72
141(chain A and (resid 2 through 53 or resid 55...A74 - 93
151(chain A and (resid 2 through 53 or resid 55...A147 - 18189
161(chain A and (resid 2 through 53 or resid 55...A191 - 243
171(chain A and (resid 2 through 53 or resid 55...A245 - 286
181(chain A and (resid 2 through 53 or resid 55...A301
211(chain B and (resid 2 through 53 or resid 55...B2 - 53
221(chain B and (resid 2 through 53 or resid 55...B55
231(chain B and (resid 2 through 53 or resid 55...B57
241(chain B and (resid 2 through 53 or resid 55...B147 - 183
251(chain B and (resid 2 through 53 or resid 55...B191 - 243
261(chain B and (resid 2 through 53 or resid 55...B245 - 286
271(chain B and (resid 2 through 53 or resid 55...B301
311(chain C and (resid 2 through 53 or resid 55...C2 - 53
321(chain C and (resid 2 through 53 or resid 55...C55
331(chain C and (resid 2 through 53 or resid 55...C57
341(chain C and (resid 2 through 53 or resid 55...C147 - 181
351(chain C and (resid 2 through 53 or resid 55...C191 - 243
361(chain C and (resid 2 through 53 or resid 55...C2 - 286
371(chain C and (resid 2 through 53 or resid 55...C191 - 243
381(chain C and (resid 2 through 53 or resid 55...C245 - 286
391(chain C and (resid 2 through 53 or resid 55...C301
411(chain D and (resid 2 through 53 or resid 55...D2 - 53
421(chain D and (resid 2 through 53 or resid 55...D55
431(chain D and (resid 2 through 53 or resid 55...D57
441(chain D and (resid 2 through 53 or resid 55...D147 - 181
451(chain D and (resid 2 through 53 or resid 55...D191 - 243
461(chain D and (resid 2 through 53 or resid 55...D2 - 286
471(chain D and (resid 2 through 53 or resid 55...D191 - 243
481(chain D and (resid 2 through 53 or resid 55...D245 - 286
491(chain D and (resid 2 through 53 or resid 55...D301

-
Components

#1: Protein
Glucokinase / N-acetylmannosamine kinase / ROK family protein


Mass: 31584.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: bglK, EP54_02970, EQ90_08795, NCTC10654_00349, NCTC10702_00557, RK64_02145
Production host: Escherichia coli (E. coli)
References: UniProt: A0A266CX40, UniProt: Q2G159*PLUS, glucokinase, beta-glucoside kinase
#2: Sugar
ChemComp-BM3 / 2-acetamido-2-deoxy-alpha-D-mannopyranose / N-acetyl-alpha-D-mannosamine / 2-acetamido-2-deoxy-alpha-D-mannose / 2-acetamido-2-deoxy-D-mannose / 2-acetamido-2-deoxy-mannose / 2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-MANNOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-mannopyranosamineCOMMON NAMEGMML 1.0
a-D-ManpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2 M L-arginine, 0.1 M sodium acetate, pH 5.0 in 8% w/v poly-gamma-glutamic acid

-
Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.2→44.556 Å / Num. obs: 124343 / % possible obs: 99.9 % / Redundancy: 2 % / CC1/2: 0.988 / Net I/σ(I): 4.9
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 6331 / CC1/2: 0.704

-
Processing

Software
NameVersionClassification
REFMACrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→44.556 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 24.87 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2317 6340 9.95 %
Rwork0.1939 --
obs0.1977 63747 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.48 Å2 / Biso mean: 52.1422 Å2 / Biso min: 25.5 Å2
Refinement stepCycle: final / Resolution: 2.2→44.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8840 0 120 89 9049
Biso mean--76.84 55.57 -
Num. residues----1140
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5205X-RAY DIFFRACTION6.025TORSIONAL
12B5205X-RAY DIFFRACTION6.025TORSIONAL
13C5205X-RAY DIFFRACTION6.025TORSIONAL
14D5205X-RAY DIFFRACTION6.025TORSIONAL
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.38020.54632.35552.3396-2.73785.6527-0.20780.2268-0.0923-0.07260.28720.2523-0.0713-0.2138-0.09130.424-0.0024-0.00180.5185-0.06930.332717.51563.493141.7557
23.94690.2314-0.90650.6417-0.19611.83810.01140.06490.1018-0.02470.00960.0464-0.17480.057-0.040.322-0.0313-0.02380.3764-0.03330.332516.95545.482652.5933
32.0752-0.6378-0.12311.33460.1141.6252-0.06130.4055-0.3688-0.1543-0.02450.01990.1614-0.03450.06020.3519-0.00940.03790.488-0.10770.4339-2.3059-5.948653.7691
48.1291-0.32542.41083.1466-0.30736.93310.1558-0.1082-0.31130.7474-0.13330.21630.0630.367-0.0790.4449-0.02880.06230.39790.0270.3188-7.675311.649995.4934
51.2227-0.8691-0.29533.8152.0432.4883-0.06920.13140.00150.1066-0.07810.0527-0.08910.14260.14490.3073-0.0188-0.01730.34090.01920.2948-5.65413.23384.7186
62.48850.697-0.28682.0928-0.37942.50750.1167-0.4284-0.6370.4323-0.167-0.07830.41350.03880.04570.5486-0.00810.00550.51630.1070.4791-0.0285-10.462982.5752
77.6703-6.2286-6.58968.10236.88787.9384-0.1688-0.3769-0.20790.4410.198-0.02320.16570.5621-0.00790.3418-0.0273-0.05660.4930.09250.32997.83531.853983.2703
85.20492.0968-2.0565.2525-0.62678.299-0.0123-0.2680.56230.1302-0.04990.0115-0.04420.12660.0740.34370.0707-0.02780.27050.01760.344514.4318-5.429828.8765
93.1629-0.60470.55023.7339-2.83835.7277-0.11310.05840.0723-0.1807-0.2042-0.350.45540.14570.30950.38290.01880.03490.3011-0.0270.325317.4604-9.652120.8564
104.50470.2155-0.78673.865-0.86394.1468-0.073-0.25870.16450.03560.01050.2087-0.0985-0.16810.06680.35410.0635-0.03920.4050.00090.26366.6113.54619.0873
114.08020.46560.33774.00081.62384.4372-0.141-0.90331.26830.5563-0.19880.1965-0.7073-0.17420.23860.68080.0457-0.10780.5123-0.20010.7128.271619.604419.2361
123.63432.0817-1.02365.75241.16213.30570.039-0.88140.8160.55290.07090.1921-0.2769-0.3539-0.07190.43980.1224-0.06850.6189-0.21630.5095-0.769613.172316.6989
138.3354-6.51556.62758.8987-6.81035.9707-0.0446-0.63280.06920.05950.12260.20420.1103-0.77650.0590.46120.05180.05090.6216-0.13750.3783-0.77694.084216.6328
143.7552-0.4063-3.30324.00583.86829.4034-0.14560.43840.00060.00060.1336-0.36830.37050.0547-0.09480.3927-0.06030.0130.42270.06260.4362-10.84812.6972108.3018
155.0965-0.17921.21470.27680.51851.3883-0.08590.0131-0.145-0.06280.0890.00370.2196-0.1442-0.01440.4225-0.07030.01430.39420.08070.3739-10.25010.6856119.2278
162.2493-0.1940.15871.41590.06752.1388-0.18310.34550.4365-0.20550.0467-0.0095-0.27440.10610.15040.4464-0.0366-0.09270.46040.13470.50149.035212.229120.541
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 39 )A2 - 39
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 151 )A40 - 151
3X-RAY DIFFRACTION3chain 'A' and (resid 152 through 286 )A152 - 286
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 39 )B2 - 39
5X-RAY DIFFRACTION5chain 'B' and (resid 40 through 151 )B40 - 151
6X-RAY DIFFRACTION6chain 'B' and (resid 152 through 260 )B152 - 260
7X-RAY DIFFRACTION7chain 'B' and (resid 261 through 286 )B261 - 286
8X-RAY DIFFRACTION8chain 'C' and (resid 2 through 39 )C2 - 39
9X-RAY DIFFRACTION9chain 'C' and (resid 40 through 119 )C40 - 119
10X-RAY DIFFRACTION10chain 'C' and (resid 120 through 170 )C120 - 170
11X-RAY DIFFRACTION11chain 'C' and (resid 171 through 231 )C171 - 231
12X-RAY DIFFRACTION12chain 'C' and (resid 232 through 260 )C232 - 260
13X-RAY DIFFRACTION13chain 'C' and (resid 261 through 286 )C261 - 286
14X-RAY DIFFRACTION14chain 'D' and (resid 2 through 39 )D2 - 39
15X-RAY DIFFRACTION15chain 'D' and (resid 40 through 151 )D40 - 151
16X-RAY DIFFRACTION16chain 'D' and (resid 152 through 286 )D152 - 286

+
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://pdbjlvh1.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