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- PDB-6q28: Metal ROK rebel: Characterisation of N-acetylmannosamine kinase f... -

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Basic information

Entry
Database: PDB / ID: 6q28
TitleMetal ROK rebel: Characterisation of N-acetylmannosamine kinase from the pathogen Staphylococcus aureus
ComponentsN-acetylmannosamine kinase
KeywordsTRANSFERASE / ROK Kinase / ROK
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCoombes, D. / Horne, C.R. / 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 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetylmannosamine kinase
B: N-acetylmannosamine kinase
C: N-acetylmannosamine kinase
D: N-acetylmannosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,7498
Polymers126,8644
Non-polymers8854
Water4,936274
1
A: N-acetylmannosamine kinase
B: N-acetylmannosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8754
Polymers63,4322
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: N-acetylmannosamine kinase
D: N-acetylmannosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8754
Polymers63,4322
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: N-acetylmannosamine kinase
hetero molecules

D: N-acetylmannosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8754
Polymers63,4322
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area4390 Å2
ΔGint0 kcal/mol
Surface area24260 Å2
MethodPISA
4
B: N-acetylmannosamine kinase
C: N-acetylmannosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8754
Polymers63,4322
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-0 kcal/mol
Surface area24170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.880, 101.968, 133.275
Angle α, β, γ (deg.)90.000, 90.140, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 19 or resid 21...
21(chain B and (resid 1 through 19 or resid 21...
31(chain C and (resid 1 through 19 or resid 21...
41(chain D and (resid 1 through 19 or resid 21...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETASPASP(chain A and (resid 1 through 19 or resid 21...AA1 - 191 - 19
12GLNGLNASNASN(chain A and (resid 1 through 19 or resid 21...AA21 - 3521 - 35
13SERSERLYSLYS(chain A and (resid 1 through 19 or resid 21...AA37 - 9337 - 93
14METMETGLNGLN(chain A and (resid 1 through 19 or resid 21...AA1 - 2861 - 286
15ASPASPGLNGLN(chain A and (resid 1 through 19 or resid 21...AA264 - 286264 - 286
16METMETGLNGLN(chain A and (resid 1 through 19 or resid 21...AA1 - 2861 - 286
17ASPASPGLNGLN(chain A and (resid 1 through 19 or resid 21...AA264 - 286264 - 286
18NAGNAGNAGNAG(chain A and (resid 1 through 19 or resid 21...AE301
21METMETASPASP(chain B and (resid 1 through 19 or resid 21...BB1 - 191 - 19
22GLNGLNASNASN(chain B and (resid 1 through 19 or resid 21...BB21 - 3521 - 35
23SERSERLYSLYS(chain B and (resid 1 through 19 or resid 21...BB37 - 9337 - 93
24METMETGLNGLN(chain B and (resid 1 through 19 or resid 21...BB1 - 2861 - 286
25ASPASPGLNGLN(chain B and (resid 1 through 19 or resid 21...BB264 - 286264 - 286
26METMETGLNGLN(chain B and (resid 1 through 19 or resid 21...BB1 - 2861 - 286
27ASPASPGLNGLN(chain B and (resid 1 through 19 or resid 21...BB264 - 286264 - 286
28NAGNAGNAGNAG(chain B and (resid 1 through 19 or resid 21...BF301
31METMETASPASP(chain C and (resid 1 through 19 or resid 21...CC1 - 191 - 19
32GLNGLNASNASN(chain C and (resid 1 through 19 or resid 21...CC21 - 3521 - 35
33SERSERLYSLYS(chain C and (resid 1 through 19 or resid 21...CC37 - 9337 - 93
34METMETGLNGLN(chain C and (resid 1 through 19 or resid 21...CC1 - 2861 - 286
35ASPASPGLNGLN(chain C and (resid 1 through 19 or resid 21...CC264 - 286264 - 286
36METMETGLNGLN(chain C and (resid 1 through 19 or resid 21...CC1 - 2861 - 286
37ASPASPGLNGLN(chain C and (resid 1 through 19 or resid 21...CC264 - 286264 - 286
38NAGNAGNAGNAG(chain C and (resid 1 through 19 or resid 21...CG301
41METMETASPASP(chain D and (resid 1 through 19 or resid 21...DD1 - 191 - 19
42GLNGLNASNASN(chain D and (resid 1 through 19 or resid 21...DD21 - 3521 - 35
43SERSERLYSLYS(chain D and (resid 1 through 19 or resid 21...DD37 - 9337 - 93
44METMETGLNGLN(chain D and (resid 1 through 19 or resid 21...DD1 - 2861 - 286
45ASPASPGLNGLN(chain D and (resid 1 through 19 or resid 21...DD264 - 286264 - 286
46METMETGLNGLN(chain D and (resid 1 through 19 or resid 21...DD1 - 2861 - 286
47ASPASPGLNGLN(chain D and (resid 1 through 19 or resid 21...DD264 - 286264 - 286
48NAGNAGNAGNAG(chain D and (resid 1 through 19 or resid 21...DH301

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Components

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


Mass: 31716.051 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: C3B39_09365, EP54_02970, EQ90_08795 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A266CX40, UniProt: Q2G159*PLUS, glucokinase, beta-glucoside kinase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2 M L-arginine, 0.1 M sodium acetate, 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: Feb 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.2→47.88 Å / Num. obs: 64898 / % possible obs: 99.8 % / Redundancy: 3.9 % / CC1/2: 0.881 / Net I/σ(I): 5.3
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 6477 / CC1/2: 0.701

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→47.88 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 27.54
RfactorNum. reflection% reflection
Rfree0.2503 3202 4.93 %
Rwork0.2081 --
obs0.2101 64886 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 105.93 Å2 / Biso mean: 38.2808 Å2 / Biso min: 17.75 Å2
Refinement stepCycle: final / Resolution: 2.2→47.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8896 0 60 274 9230
Biso mean--55.13 48.27 -
Num. residues----1144
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3344X-RAY DIFFRACTION6.348TORSIONAL
12B3344X-RAY DIFFRACTION6.348TORSIONAL
13C3344X-RAY DIFFRACTION6.348TORSIONAL
14D3344X-RAY DIFFRACTION6.348TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.23280.40841420.34262635100
2.2328-2.26770.31771300.31862722100
2.2677-2.30490.35191410.30562628100
2.3049-2.34470.29961380.287264599
2.3447-2.38730.33131600.28322699100
2.3873-2.43320.26751220.26282636100
2.4332-2.48290.35841370.26782683100
2.4829-2.53680.27981530.2712674100
2.5368-2.59590.3341310.25742628100
2.5959-2.66080.28581220.24312727100
2.6608-2.73270.28521490.24472654100
2.7327-2.81310.30931310.24682702100
2.8131-2.90390.29081340.23632649100
2.9039-3.00770.2641350.24542731100
3.0077-3.12810.28571440.23692625100
3.1281-3.27040.24141450.21532700100
3.2704-3.44280.24131210.20222737100
3.4428-3.65840.27031640.19972644100
3.6584-3.94080.22741690.18092663100
3.9408-4.33710.18821140.15912730100
4.3371-4.96410.17841340.13552693100
4.9641-6.25210.20881500.15022710100
6.2521-47.880.1691360.15632769100
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)
14.81130.1122-0.12491.22680.35863.48890.0377-0.1859-0.12570.0688-0.0608-0.1011-0.1278-0.13060.0060.27070.0141-0.02190.19130.00950.2468-9.3439-0.07177.4144
21.54150.163-0.3950.5503-0.17521.6672-0.003-0.1394-0.07830.0743-0.06590.05740.03010.03870.05280.3238-0-0.00520.2182-0.01180.284112.6243-7.5999-0.453
33.9119-3.9656-3.40574.55112.28316.77560.1407-0.04940.385-0.0262-0.1111-0.6089-0.06480.1216-0.06210.3959-0.0494-0.02510.2652-0.05590.3434-0.7961-11.235627.1504
41.94220.0781-0.03872.90220.50675.32940.08740.1371-0.0268-0.17710.04660.25720.6972-0.3016-0.12370.3886-0.0525-0.0290.23090.03910.3088-5.0299-12.870331.9891
53.01040.1648-0.67061.59220.88922.9526-0.0820.2858-0.2592-0.10270.1198-0.14230.09790.1954-0.04140.3035-0.02070.0160.3534-0.04280.24534.41250.554245.7387
61.5804-2.0342.13013.8542-4.27934.56730.22220.0539-0.2295-0.76120.11820.13810.743-0.2771-0.37340.49530.0705-0.0840.38140.03740.2748-4.118214.367836.3457
72.7705-2.48711.25163.9809-2.36892.22540.2580.43710.0771-0.3814-0.390.102-0.04460.29140.15170.3619-0.0045-0.04380.39640.00410.26387.148114.627835.503
83.72813.38983.30985.29085.9798.2277-0.04960.3878-0.0561-0.12560.1372-0.0882-0.01540.4893-0.05340.33390.06850.00280.3960.07170.289312.01631.598438.3369
97.09691.3482-1.32266.8067-0.89627.465-0.0187-0.00890.00080.51050.01540.20830.1614-0.229-0.05850.26420.0209-0.00780.2461-0.00060.228921.4387-0.13379.5901
106.0001-0.85952.34312.79790.02463.6471-0.0164-0.8388-0.00860.24540.08010.04950.17130.2005-0.11130.2940.01180.0470.29770.01040.244728.9253-2.170577.5323
116.5772-0.28971.7692-0.1404-0.0941.3798-0.0260.04890.0638-0.0562-0.0930.05930.04010.11460.09160.33410.03670.01330.1739-0.00440.320524.22030.471367.2594
127.86860.9102-0.93722.14270.13624.2549-0.0585-0.1522-0.5942-0.001-0.0555-0.03850.43650.08750.0850.26790.0351-0.00360.29430.0410.31187.8371-4.293562.0186
132.3675-0.5854-2.21960.18330.66654.65840.0917-0.21820.13260.0544-0.01060.217-0.47830.3781-0.11460.3452-0.0589-0.05120.2625-0.0110.31778.253216.037361.9112
142.1359-0.7904-0.28675.78954.71048.1996-0.0814-0.23820.29690.2685-0.37160.3553-0.4175-0.51710.32380.3707-0.0065-0.02160.1802-0.01650.3524-2.360714.74471.1994
153.7457-2.7042-0.07023.5929-0.95411.433-0.2404-0.47640.23310.22750.08920.1556-0.0902-0.11690.17870.2841-0.0272-0.01450.2174-0.05930.2913-3.23344.957967.7166
166.1352-1.58865.47541.7519-1.59555.18330.2385-0.3961-0.15590.07770.0282-0.11580.322-0.2819-0.28640.3228-0.02070.01350.2914-0.00680.28332.7742-1.896767.3081
177.7458-4.25322.07467.6434-0.40558.33110.15170.0140.3236-0.84890.0043-0.3828-0.59410.2701-0.11240.4178-0.08390.04780.2406-0.00680.269317.66029.694492.5031
182.48980.7151-0.57855.6761-1.98233.8131-0.0056-0.10130.0464-0.50180.3257-0.6588-0.90630.8842-0.13040.5292-0.15910.08990.2453-0.10070.418123.380212.888699.7245
193.03661.2996-1.52165.0767-1.2261.9042-0.1770.0880.3617-0.13990.3131-0.0509-0.88170.0968-0.11680.6031-0.1016-0.04060.1943-0.02440.357916.01814.0826102.7445
207.391.48992.72083.19381.25355.9791-0.07250.16220.6424-0.055-0.0420.1675-0.4109-0.93470.11340.287-0.003-0.00170.34270.0720.2865.20683.5703110.4204
210.60930.2710.91473.58132.47442.3028-0.05590.0856-0.1513-0.41110.1444-0.1859-0.04310.1653-0.10810.3330.00230.04790.3831-0.02480.31519.2154-11.1325109.9408
222.8779-2.2059-1.20445.15324.24516.40190.25520.5582-0.1356-0.435-0.0366-0.30930.0723-0.1007-0.22350.4641-0.08790.04940.2766-0.05450.353310.2847-17.1386100.6842
232.9094-1.47120.45698.95132.14715.90210.04270.5886-0.3467-0.6722-0.31640.07890.276-0.21220.24850.2939-0.03820.0060.3398-0.06440.26933.3135-10.5528104.3706
245.79914.2185-3.6735.3893-4.93855.0364-0.0750.01290.2442-0.30510.04170.06380.0439-0.3918-0.08450.33780.045-0.01280.3938-0.02990.25752.978-1.625104.9105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 119 )A1 - 119
2X-RAY DIFFRACTION2chain 'A' and (resid 120 through 286 )A120 - 286
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 18 )B1 - 18
4X-RAY DIFFRACTION4chain 'B' and (resid 19 through 119 )B19 - 119
5X-RAY DIFFRACTION5chain 'B' and (resid 120 through 170 )B120 - 170
6X-RAY DIFFRACTION6chain 'B' and (resid 171 through 186 )B171 - 186
7X-RAY DIFFRACTION7chain 'B' and (resid 187 through 260 )B187 - 260
8X-RAY DIFFRACTION8chain 'B' and (resid 261 through 286 )B261 - 286
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 39 )C1 - 39
10X-RAY DIFFRACTION10chain 'C' and (resid 40 through 71 )C40 - 71
11X-RAY DIFFRACTION11chain 'C' and (resid 72 through 119 )C72 - 119
12X-RAY DIFFRACTION12chain 'C' and (resid 120 through 151 )C120 - 151
13X-RAY DIFFRACTION13chain 'C' and (resid 152 through 186 )C152 - 186
14X-RAY DIFFRACTION14chain 'C' and (resid 187 through 231 )C187 - 231
15X-RAY DIFFRACTION15chain 'C' and (resid 232 through 260 )C232 - 260
16X-RAY DIFFRACTION16chain 'C' and (resid 261 through 286 )C261 - 286
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 39 )D1 - 39
18X-RAY DIFFRACTION18chain 'D' and (resid 40 through 91 )D40 - 91
19X-RAY DIFFRACTION19chain 'D' and (resid 92 through 119 )D92 - 119
20X-RAY DIFFRACTION20chain 'D' and (resid 120 through 151 )D120 - 151
21X-RAY DIFFRACTION21chain 'D' and (resid 152 through 186 )D152 - 186
22X-RAY DIFFRACTION22chain 'D' and (resid 187 through 231 )D187 - 231
23X-RAY DIFFRACTION23chain 'D' and (resid 232 through 260 )D232 - 260
24X-RAY DIFFRACTION24chain 'D' and (resid 261 through 286 )D261 - 286

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

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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

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