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- PDB-6q26: N-Acetylmannosamine kinase from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 6q26
TitleN-Acetylmannosamine kinase from Staphylococcus aureus
ComponentsGlucokinase
KeywordsTRANSFERASE / Ribonuclease H-like Motif / ROK family protein / ROK Kinase
Function / homologybeta-glucoside kinase / beta-glucoside kinase activity / glucokinase / ROK family / ROK family / glucokinase activity / ATPase, nucleotide binding domain / Glucokinase / ROK family protein
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.328 Å
AuthorsCoombes, D. / North, R.A. / 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: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)127,9904
Polymers127,9904
Non-polymers00
Water5,314295
1
A: Glucokinase
B: Glucokinase


Theoretical massNumber of molelcules
Total (without water)63,9952
Polymers63,9952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-14 kcal/mol
Surface area25740 Å2
MethodPISA
2
D: Glucokinase
C: Glucokinase


Theoretical massNumber of molelcules
Total (without water)63,9952
Polymers63,9952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-13 kcal/mol
Surface area25780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.647, 135.149, 175.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-367-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 27 or resid 34...
21(chain B and (resid 1 through 27 or resid 34...
31(chain C and (resid 1 through 27 or resid 34...
41(chain D and (resid 1 through 45 or resid 47...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 27 or resid 34...A1 - 27
121(chain A and (resid 1 through 27 or resid 34...A34 - 45
131(chain A and (resid 1 through 27 or resid 34...A47 - 52
141(chain A and (resid 1 through 27 or resid 34...A54 - 72
151(chain A and (resid 1 through 27 or resid 34...A86 - 122
161(chain A and (resid 1 through 27 or resid 34...A1 - 286
171(chain A and (resid 1 through 27 or resid 34...A147 - 153
181(chain A and (resid 1 through 27 or resid 34...A1 - 286
191(chain A and (resid 1 through 27 or resid 34...A155 - 189
1101(chain A and (resid 1 through 27 or resid 34...A192
1111(chain A and (resid 1 through 27 or resid 34...A1 - 286
1121(chain A and (resid 1 through 27 or resid 34...A231 - 273
1131(chain A and (resid 1 through 27 or resid 34...A275 - 286
211(chain B and (resid 1 through 27 or resid 34...B1 - 27
221(chain B and (resid 1 through 27 or resid 34...B34 - 45
231(chain B and (resid 1 through 27 or resid 34...B47 - 52
241(chain B and (resid 1 through 27 or resid 34...B54 - 72
251(chain B and (resid 1 through 27 or resid 34...B74 - 81
261(chain B and (resid 1 through 27 or resid 34...B86 - 122
271(chain B and (resid 1 through 27 or resid 34...B124 - 141
281(chain B and (resid 1 through 27 or resid 34...B145
291(chain B and (resid 1 through 27 or resid 34...B147 - 153
2101(chain B and (resid 1 through 27 or resid 34...B155 - 189
2111(chain B and (resid 1 through 27 or resid 34...B192
2121(chain B and (resid 1 through 27 or resid 34...B1 - 286
2131(chain B and (resid 1 through 27 or resid 34...B231 - 273
2141(chain B and (resid 1 through 27 or resid 34...B1 - 286
2151(chain B and (resid 1 through 27 or resid 34...B275 - 286
311(chain C and (resid 1 through 27 or resid 34...C1 - 27
321(chain C and (resid 1 through 27 or resid 34...C34 - 45
331(chain C and (resid 1 through 27 or resid 34...C47 - 52
341(chain C and (resid 1 through 27 or resid 34...C86 - 122
351(chain C and (resid 1 through 27 or resid 34...C124 - 141
361(chain C and (resid 1 through 27 or resid 34...C1 - 286
371(chain C and (resid 1 through 27 or resid 34...C145
381(chain C and (resid 1 through 27 or resid 34...C147 - 153
391(chain C and (resid 1 through 27 or resid 34...C192
3101(chain C and (resid 1 through 27 or resid 34...C1 - 286
3111(chain C and (resid 1 through 27 or resid 34...C1 - 286
3121(chain C and (resid 1 through 27 or resid 34...C1 - 286
3131(chain C and (resid 1 through 27 or resid 34...C231 - 273
3141(chain C and (resid 1 through 27 or resid 34...C275 - 286
411(chain D and (resid 1 through 45 or resid 47...D1 - 45
421(chain D and (resid 1 through 45 or resid 47...D47 - 52
431(chain D and (resid 1 through 45 or resid 47...D54 - 72
441(chain D and (resid 1 through 45 or resid 47...D74 - 122
451(chain D and (resid 1 through 45 or resid 47...D147 - 153
461(chain D and (resid 1 through 45 or resid 47...D192
471(chain D and (resid 1 through 45 or resid 47...D192
481(chain D and (resid 1 through 45 or resid 47...D195 - 205
491(chain D and (resid 1 through 45 or resid 47...D207 - 229

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Components

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


Mass: 31997.414 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
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: 2.7 Å3/Da / Density % sol: 54.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Molecular Dimensions JCSG G6: 0.2 M sodium malonate dibasic monohydrate 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9724 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2016 / Details: mx@
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.328→48.736 Å / Num. obs: 867330 / % possible obs: 99.9 % / Redundancy: 14.6 % / CC1/2: 0.994 / Net I/σ(I): 20
Reflection shellResolution: 2.328→2.412 Å / Num. unique obs: 5864 / CC1/2: 0.671

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
Aimlessdata scaling
SHELXDEphasing
BUCCANEERmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.328→48.736 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 23.35
RfactorNum. reflection% reflection
Rfree0.24 6037 10.16 %
Rwork0.1974 --
obs0.2017 59448 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.12 Å2 / Biso mean: 37.0943 Å2 / Biso min: 10.74 Å2
Refinement stepCycle: final / Resolution: 2.328→48.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8808 0 0 295 9103
Biso mean---32.33 -
Num. residues----1131
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2864X-RAY DIFFRACTION1.397TORSIONAL
12B2864X-RAY DIFFRACTION1.397TORSIONAL
13C2864X-RAY DIFFRACTION1.397TORSIONAL
14D2864X-RAY DIFFRACTION1.397TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3284-2.35490.34852030.2918173998
2.3549-2.38260.32912050.26331738100
2.3826-2.41160.30912140.25911765100
2.4116-2.44220.29381760.25091750100
2.4422-2.47430.28732020.24381789100
2.4743-2.50820.32922050.23811733100
2.5082-2.5440.28541930.23771805100
2.544-2.5820.28731920.22941745100
2.582-2.62230.27612060.21871780100
2.6223-2.66530.27522040.22151741100
2.6653-2.71130.27412060.22211784100
2.7113-2.76060.29081930.22091759100
2.7606-2.81370.30761530.22311801100
2.8137-2.87110.24871940.2171798100
2.8711-2.93350.28332080.23221753100
2.9335-3.00170.28522010.23281759100
3.0017-3.07680.27462270.23191791100
3.0768-3.160.28392100.21671728100
3.16-3.25290.23822060.20561771100
3.2529-3.35790.2261850.19851790100
3.3579-3.47790.23841860.19621801100
3.4779-3.61710.2352160.1951764100
3.6171-3.78170.23852100.1871784100
3.7817-3.9810.23372110.18011782100
3.981-4.23020.18081960.16821807100
4.2302-4.55660.18361950.13911788100
4.5566-5.01480.19842050.15591816100
5.0148-5.73950.18692180.16631799100
5.7395-7.22730.20471980.19151842100
7.2273-48.7360.19072190.1661909100
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)
12.56950.3716-0.45341.67230.2161.09990.1224-0.02020.2570.09850.02890.3229-0.1192-0.1423-0.14750.2478-0.01010.0770.22290.01670.3016-43.4705-14.509-10.5467
21.49261.0981-0.35853.0997-0.55610.1376-0.0518-0.0291-0.0003-0.35710.05520.1178-0.02870.07270.00830.231-0.00310.01730.2072-0.00920.2204-24.0339-21.9347-10.1419
31.02840.6369-0.09161.71760.39811.71090.0258-0.02160.05230.20660.054-0.0171-0.04320.0724-0.05410.23460.0057-0.00280.2353-0.00680.1907-18.5279-15.19549.4491
40.91520.22780.56780.8537-0.0371.59280.0023-0.12210.0965-0.05220.1051-0.1101-0.21230.0349-0.11480.2331-0.03220.06080.234-0.03230.2375-16.8203-13.9338-5.0013
50.4671-0.15770.11750.21810.35650.8589-0.35211.347-0.2904-0.7050.6412-0.6245-0.50030.9532-0.31720.5906-0.52610.36181.0848-0.310.4017-9.2497-7.6033-32.7716
60.7630.1281-0.72631.06510.73771.27230.01210.15770.1247-0.66650.19340.1532-0.7630.1399-0.05340.6596-0.0956-0.01610.25710.01960.2775-33.1616-13.6639-45.7435
76.2432.37743.12093.2791.85063.2377-0.22190.23210.2299-0.41750.19510.3059-0.69920.17720.04750.3585-0.02340.01580.2261-0.01120.1384-34.155-13.4158-35.6681
82.1391-0.40370.04681.8902-0.2131.11540.1132-0.0895-0.67240.07960.16060.71270.2987-0.4229-0.20910.3049-0.1137-0.00860.36450.04040.5342-44.1379-49.3598-23.6495
91.0572-1.05550.09641.26750.06131.96930.0730.11350.1030.04430.039-0.01470.11720.1284-0.15560.2236-0.0103-0.02010.2725-0.06290.2218-30.0132-42.0248-34.6739
103.1016-1.6038-1.99023.67060.24941.48950.0685-0.2610.08670.31370.24-0.2564-0.1320.5637-0.11370.2515-0.0004-0.00380.2952-0.05560.2778-33.9804-31.9626-33.6811
110.35030.03470.26860.63970.85282.1834-0.01110.00150.0528-0.19850.09870.0140.02150.2244-0.08840.2445-0.0453-0.01960.2751-0.02990.2358-31.254-42.6004-51.2887
120.9790.4167-0.36010.99190.56111.78010.0250.1678-0.15390.06020.238-0.37210.15680.3673-0.23080.25030.0501-0.03860.3603-0.13450.3733-5.0442-43.1942-24.6155
131.35020.7525-1.66194.1921-0.80992.44410.06970.4063-0.0622-0.4770.2760.16350.1073-0.1011-0.02890.2185-0.0209-0.00190.2702-0.04990.2872-15.1776-31.6745-14.6127
141.9835-0.39490.50770.9658-0.05711.00330.1108-0.1413-0.2944-0.00140.0431-0.06150.13640.0111-0.13050.2209-0.0025-0.05490.21910.00540.29-13.1706-45.75173.9615
151.6750.0844-0.90760.99480.19683.0514-0.0860.0677-0.3127-0.055-0.04220.03980.35910.0057-0.04840.23190.0124-0.05290.1527-0.02330.2963-20.394-44.6161-10.552
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 118 )A1 - 118
2X-RAY DIFFRACTION2chain 'A' and (resid 119 through 160 )A119 - 160
3X-RAY DIFFRACTION3chain 'A' and (resid 161 through 231 )A161 - 231
4X-RAY DIFFRACTION4chain 'A' and (resid 232 through 286 )A232 - 286
5X-RAY DIFFRACTION5chain 'D' and (resid 1 through 102 )D1 - 102
6X-RAY DIFFRACTION6chain 'D' and (resid 103 through 260 )D103 - 260
7X-RAY DIFFRACTION7chain 'D' and (resid 261 through 286 )D261 - 286
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 102 )C1 - 102
9X-RAY DIFFRACTION9chain 'C' and (resid 103 through 138 )C103 - 138
10X-RAY DIFFRACTION10chain 'C' and (resid 139 through 160 )C139 - 160
11X-RAY DIFFRACTION11chain 'C' and (resid 161 through 286 )C161 - 286
12X-RAY DIFFRACTION12chain 'B' and (resid 1 through 138 )B1 - 138
13X-RAY DIFFRACTION13chain 'B' and (resid 139 through 160 )B139 - 160
14X-RAY DIFFRACTION14chain 'B' and (resid 161 through 260 )B161 - 260
15X-RAY DIFFRACTION15chain 'B' and (resid 261 through 286 )B261 - 286

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