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- PDB-6q27: N-acetylmannosamine kinase with N-acetylmannosamine from Staphylo... -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 2.52 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

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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

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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

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