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- PDB-5ih0: Macrolide 2'-phosphotransferase type II Y92M mutant - complex wit... -

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Basic information

Entry
Database: PDB / ID: 5ih0
TitleMacrolide 2'-phosphotransferase type II Y92M mutant - complex with GDP and erythromycin
ComponentsMacrolide 2'-phosphotransferase II
KeywordsTRANSFERASE/ANTIBIOTIC / macrolide phosphotransferase / kinase / TRANSFERASE / TRANSFERASE-ANTIBIOTIC complex
Function / homologyAminoglycoside phosphotransferase / Phosphotransferase enzyme family / transferase activity / Protein kinase-like domain superfamily / metal ion binding / ACETATE ION / ERYTHROMYCIN A / GUANOSINE-5'-DIPHOSPHATE / Macrolide 2'-phosphotransferase II
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBerghuis, A.M. / Fong, D.H.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-13107 Canada
CitationJournal: Structure / Year: 2017
Title: Structural Basis for Kinase-Mediated Macrolide Antibiotic Resistance.
Authors: Fong, D.H. / Burk, D.L. / Blanchet, J. / Yan, A.Y. / Berghuis, A.M.
History
DepositionFeb 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2May 17, 2017Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Macrolide 2'-phosphotransferase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7565
Polymers34,4951
Non-polymers1,2604
Water8,125451
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-22 kcal/mol
Surface area14490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.920, 80.090, 96.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Macrolide 2'-phosphotransferase II / Macrolide 2'-phosphotransferase II protein MphB / Macrolide 2-phosphotransferase / mph(B)


Mass: 34495.234 Da / Num. of mol.: 1 / Mutation: Y92M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BM2506 / Gene: mphB, pO103_99 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O32553

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Non-polymers , 5 types, 455 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-ERY / ERYTHROMYCIN A


Mass: 733.927 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H67NO13 / Comment: antibiotic*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1 M calcium acetate, 0.1M Tris, 25-40% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 13, 2011
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.65→41.395 Å / Num. obs: 38102 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Net I/σ(I): 25.93
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.65-1.690.5722.791100
1.69-1.740.4483.851100
1.74-1.790.44.411100
1.79-1.840.2935.971100
1.84-1.910.2357.67199.8
1.91-1.970.16211.64199.7
1.97-2.050.12714.151100
2.05-2.130.118.64199.9
2.13-2.220.07723.651100
2.22-2.330.06727.43199.5
2.33-2.460.05531.78199.9
2.46-2.610.04637.54199.9
2.61-2.790.03942.69199.9
2.79-3.010.03548.58199.9
3.01-3.30.02957.33199.9
3.3-3.690.02563.731100
3.69-4.260.02268.59199.9
4.26-5.220.0270.54199.9
5.22-7.380.01867.871100
7.380.01769.91199.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IWU

5iwu


Resolution: 1.65→41.395 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 20.35
RfactorNum. reflection% reflection
Rfree0.2098 1902 4.99 %
Rwork0.1818 --
obs0.1832 38086 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.23 Å2 / Biso mean: 24.66 Å2 / Biso min: 3.66 Å2
Refinement stepCycle: final / Resolution: 1.65→41.395 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2393 0 166 451 3010
Biso mean--21.42 31.54 -
Num. residues----299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042593
X-RAY DIFFRACTIONf_angle_d0.8743541
X-RAY DIFFRACTIONf_chiral_restr0.046390
X-RAY DIFFRACTIONf_plane_restr0.003447
X-RAY DIFFRACTIONf_dihedral_angle_d15.582931
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.65-1.69130.26081340.245125462680
1.6913-1.7370.27561330.223825572690
1.737-1.78810.26781330.220425242657
1.7881-1.84580.25141330.212825322665
1.8458-1.91180.25761360.217325722708
1.9118-1.98830.24291320.205425432675
1.9883-2.07880.24111350.192325542689
2.0788-2.18840.20971350.183125742709
2.1884-2.32550.21321350.184225682703
2.3255-2.50510.20391360.176125942730
2.5051-2.75710.20831370.174325902727
2.7571-3.15590.20221370.174225992736
3.1559-3.97570.18131390.15526542793
3.9757-41.40830.17841470.169627772924
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)
15.17490.0986-1.48762.16681.67275.27360.0186-0.7072-0.41960.6249-0.1678-0.18390.6699-0.12160.11950.5263-0.0099-0.15350.31370.030.21999.6022-11.043752.0602
21.7693-0.5628-1.41554.53881.81961.5643-0.2119-0.20810.10530.3303-0.46130.5829-0.0403-0.6850.62910.3850.0422-0.05340.4597-0.14570.22212.0906-8.154546.2085
31.43790.73261.14935.11571.60193.6432-0.20540.12790.0777-0.03060.00330.0925-0.1094-0.24690.12530.24060.0514-0.05890.2314-0.0660.10746.3463-7.580842.5089
40.4774-0.90620.83892.2488-1.81471.6281-0.04850.02220.080.0584-0.0386-0.30790.06160.08220.07280.08980.0043-0.00210.1377-0.01060.175910.433-6.922529.641
54.76260.3287-1.78591.10930.53366.0782-0.0784-0.36470.00980.29430.0199-0.67950.22780.28050.06310.14770.0105-0.07640.11360.01630.230513.496-10.250939.047
62.5013-1.88591.64581.44-1.28581.1935-0.0895-0.50270.25060.29110.0582-0.2371-0.1827-0.12840.02540.21780.0648-0.07730.2571-0.08780.15590.71841.285338.3009
71.904-0.21290.00041.55920.09921.7858-0.1905-0.2672-0.10720.20630.05350.14830.0071-0.24170.07680.11110.0240.01420.12330.01170.1259-8.83542.088927.1211
88.3866-2.28151.2173.93192.62012.8070.06230.1730.21730.00110.14790.8888-0.0144-0.6125-0.2040.09240.00010.04650.25060.05410.236817.7341-3.911516.7238
90.37950.3218-0.08170.92860.40270.955-0.13260.1725-0.2877-0.1033-0.07320.05370.288-0.1855-0.01530.2558-0.03570.12710.1971-0.10550.24982.1175-14.03459.752
100.1735-0.21740.26751.1656-0.4410.4258-0.22540.0960.0133-0.4750.08410.0478-0.07060.01220.10520.5594-0.18740.11150.3831-0.23220.6982-12.6558-23.307110.6199
110.57280.28910.2060.63840.34290.2925-0.15670.2333-0.1307-0.3379-0.09690.22280.0818-0.43140.17860.3106-0.10890.02940.4831-0.14010.1862-7.3934-9.36014.0973
121.98910.0152-0.52121.3585-0.27421.5228-0.1132-0.10490.09830.06490.0918-0.0587-0.0252-0.05420.0030.05950.01730.00050.0693-0.00590.0549-3.4503-2.005124.4043
134.2022-0.5327-2.00823.5808-0.14793.0045-0.07750.46730.3135-0.29360.17660.3007-0.1193-0.2711-0.06810.08830.0182-0.00730.1130.04920.0929-9.2436.977314.9463
142.62110.9824-0.86524.25-0.70011.3681-0.19580.3595-0.2109-0.2774-0.01990.15250.2936-0.13830.15440.1494-0.03840.0320.1515-0.03580.092-8.5548-6.897412.6877
150.7736-0.3918-0.10190.8142-0.01790.7527-0.2052-0.0167-0.22840.149-0.08650.16060.3495-0.11110.21780.6411-0.060.44020.3039-0.080.8102-12.5422-23.142423.4756
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:20)A1 - 20
2X-RAY DIFFRACTION2(chain A and resid 21:44)A21 - 44
3X-RAY DIFFRACTION3(chain A and resid 45:51)A45 - 51
4X-RAY DIFFRACTION4(chain A and resid 52:81)A52 - 81
5X-RAY DIFFRACTION5(chain A and resid 82:91)A82 - 91
6X-RAY DIFFRACTION6(chain A and resid 92:100)A92 - 100
7X-RAY DIFFRACTION7(chain A and resid 101:139)A101 - 139
8X-RAY DIFFRACTION8(chain A and resid 140:145)A140 - 145
9X-RAY DIFFRACTION9(chain A and resid 146:165)A146 - 165
10X-RAY DIFFRACTION10(chain A and resid 166:177)A166 - 177
11X-RAY DIFFRACTION11(chain A and resid 178:193)A178 - 193
12X-RAY DIFFRACTION12(chain A and resid 194:240)A194 - 240
13X-RAY DIFFRACTION13(chain A and resid 241:256)A241 - 256
14X-RAY DIFFRACTION14(chain A and resid 257:280)A257 - 280
15X-RAY DIFFRACTION15(chain A and resid 281:299)A281 - 299

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