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- PDB-5igj: Macrolide 2'-phosphotransferase type I - complex with guanosine a... -

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Basic information

Entry
Database: PDB / ID: 5igj
TitleMacrolide 2'-phosphotransferase type I - complex with guanosine and clarithromycin
ComponentsMacrolide 2'-phosphotransferase
KeywordsTRANSFERASE/ANTIBIOTIC / macrolide phosphotransferase / kinase / TRANSFERASE-ANTIBIOTIC complex
Function / homologyAminoglycoside phosphotransferase / Phosphotransferase enzyme family / transferase activity / Protein kinase-like domain superfamily / CLARITHROMYCIN / GUANOSINE / ISOPROPYL ALCOHOL / Aminoglycoside phosphotransferase
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3584
Polymers33,2671
Non-polymers1,0913
Water7,728429
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Macrolide 2'-phosphotransferase
hetero molecules

A: Macrolide 2'-phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7168
Polymers66,5342
Non-polymers2,1836
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_677x-y+1,-y+2,-z+7/31
Buried area5820 Å2
ΔGint-34 kcal/mol
Surface area27120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.200, 45.200, 247.100
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Macrolide 2'-phosphotransferase / Macrolide 2'-phosphotransferase I / Macrolide 2'-phosphotransferase I Mph(A) / Macrolide 2'- ...Macrolide 2'-phosphotransferase I / Macrolide 2'-phosphotransferase I Mph(A) / Macrolide 2'-phosphotransferase Mph(A) / Macrolide 2-phosphotransferase / Macrolide 2-phosphotransferase protein / macrolide resistance protein / Macrolide-phosphotransferase / mph(A) / Mph(A) / Mph(A) macrolide 2'-phosphotransferase I / Uncharacterized protein


Mass: 33266.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: Tf481A
Gene: mphA, mph(A), mph2, AM267_25240, AM268_24740, AN205_25580, AN669_16770, ASU34_20250, AZ95_0038, ECONIH1_26770, ERS085366_04054, ERS085367_04848, ERS139269_04809, ERS150873_04753, ETN48_p0083, ...Gene: mphA, mph(A), mph2, AM267_25240, AM268_24740, AN205_25580, AN669_16770, ASU34_20250, AZ95_0038, ECONIH1_26770, ERS085366_04054, ERS085367_04848, ERS139269_04809, ERS150873_04753, ETN48_p0083, orf00017, pCTXM123_C0996_11, pKC394-009, SK74_04859, SK86_03516, UN86_19875
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q47396
#2: Chemical ChemComp-GMP / GUANOSINE


Mass: 283.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O5
#3: Chemical ChemComp-CTY / CLARITHROMYCIN


Mass: 747.953 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H69NO13 / Comment: antibiotic*YM
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.2 Å3/Da / Density % sol: 44.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.2
Details: 0.1 M Na citrate, 25% PEG 4000, 20% isopropanol. 0.2 M ammonium acetate

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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-225 / Detector: CCD / Date: Oct 13, 2010
RadiationMonochromator: DCM / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.4→41.183 Å / Num. obs: 57398 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 24.77
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.4-1.440.7732.06177.2
1.44-1.480.6122.88186
1.48-1.520.5373.9197.8
1.52-1.570.4325.3198.5
1.57-1.620.3496.66198.7
1.62-1.670.2748.24199
1.67-1.740.21210.46198.9
1.74-1.810.16613.04199.3
1.81-1.890.1316.26199.3
1.89-1.980.09521.49199.4
1.98-2.090.07227.59199.7
2.09-2.210.05434.64199.7
2.21-2.370.04540.09199.9
2.37-2.560.0444.5199.9
2.56-2.80.03451.21199.9
2.8-3.130.02761.431100
3.13-3.620.02272.811100
3.62-4.430.01980.1199.9
4.43-6.260.01780.851100
6.260.01679.97199.3

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Processing

Software
NameVersionClassification
XDSMarch 5, 2012data reduction
XSCALEdata scaling
PHASERphasing
PHENIXdev_1034refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IGH

5igh


Resolution: 1.4→41.183 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 15.46
RfactorNum. reflection% reflection
Rfree0.1692 1988 3.46 %
Rwork0.1514 --
obs0.152 57397 96.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 64.61 Å2 / Biso mean: 17.73 Å2 / Biso min: 2.85 Å2
Refinement stepCycle: final / Resolution: 1.4→41.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2334 0 166 429 2929
Biso mean--16.04 29.23 -
Num. residues----300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012615
X-RAY DIFFRACTIONf_angle_d1.3973598
X-RAY DIFFRACTIONf_chiral_restr0.115413
X-RAY DIFFRACTIONf_plane_restr0.007463
X-RAY DIFFRACTIONf_dihedral_angle_d11.474932
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4004-1.43550.25961100.24433031314177
1.4355-1.47430.23941260.2143446357285
1.4743-1.51770.23521400.19033915405597
1.5177-1.56660.18181440.16814004414899
1.5666-1.62260.19821370.1643948408599
1.6226-1.68760.18721470.14893993414099
1.6876-1.76440.18241410.14563992413399
1.7644-1.85740.16151470.14554040418799
1.8574-1.97380.15211450.14314076422199
1.9738-2.12620.14491430.135940634206100
2.1262-2.34020.17351480.134241014249100
2.3402-2.67870.15711490.139641524301100
2.6787-3.37470.15761500.14541894339100
3.3747-41.20110.16311610.155644594620100
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)
10.0012-0.00040.00230.00530.00190.01090.0052-0.00870.0298-0.03840.00920.0451-0.02940.00510.00020.2465-0.1183-0.02430.25790.01110.177337.070654.2236293.4044
20.0005-0.0019-0.00120.00390.00130.00360.04330.01340.07530.1431-0.0804-0.1029-0.1795-0.0520.00010.27670.0143-0.02760.1187-0.01190.216427.715160.2904281.8788
30.00420.00240.0040.00240.00240.00290.08170.07140.00170.09530.0221-0.01750.0023-0.06930.00050.29370.06830.02920.17670.01180.153620.55456.7427285.6219
40.0101-0.0037-0.00010.0070.00580.00590.00860.0177-0.02460.01820.0286-0.00030.00120.02560.03680.07140.0914-0.17140.21730.0122-0.179529.410748.3311287.4174
50.0170.0103-0.00410.0178-0.02330.0146-0.108-0.0613-0.0014-0.018-0.0516-0.2492-0.07910.041-0.00990.11960.01940.04760.16670.04650.180132.964448.7991279.0716
60.0080.00340.00470.00180.00480.0073-0.0371-0.00070.07120.04970.09930.14870.0204-0.03160.00030.14370.04910.03570.18110.01580.1117.247149.3743283.5718
70.00760.0019-0.00070.01110.00080.0062-0.0711-0.005-0.0078-0.0732-0.0397-0.2002-0.00840.0083-0.00410.0925-0.0150.0230.17640.01860.138633.629652.0839272.4868
80.06310.01450.01690.03060.0039-0.00140.04650.0451-0.0835-0.03370.0223-0.0441-0.11260.03730.00040.1379-0.01310.01190.1615-0.0090.129324.103947.8361263.3393
90.01740.0043-0.00770.0110.01150.0105-0.04030.07480.0211-0.08970.01010.1496-0.0516-0.2157-0.00520.07160.0051-0.01830.1632-0.00460.108916.965140.5174267.9444
100.01970.01070.00430.03810.06480.0694-0.013-0.03240.04020.0223-0.00560.0392-0.0156-0.0394-0.00010.10290.0057-0.00050.11760.00340.095422.263746.9143275.9649
110.16150.01630.10570.0441-0.02350.09090.0019-0.05770.1047-0.0007-0.0274-0.05840.04220.12240.019-0.1310.0696-0.08230.06390.0343-0.007434.720431.3597282.5113
120.0363-0.0401-0.00380.04630.02580.10920.01560.0317-0.02930.0094-0.0580.0380.1661-0.0746-0.0190.0884-0.0274-0.00540.09680.01750.091121.012125.9992267.401
130.02660.0170.03780.02080.03110.04850.05890.07690.0397-0.0704-0.0728-0.0311-0.09440.0302-0.0190.07930.0087-0.0060.14510.01610.080627.676438.8137251.0741
140.07540.01860.03950.47860.24430.138-0.03680.13680.0475-0.1964-0.0895-0.0602-0.13790.2081-0.05950.0541-0.0240.01270.20510.0560.094848.33137.0461255.2616
150.03110.0019-0.00560.00650.00420.00280.07830.1185-0.0301-0.07960.0039-0.1492-0.00250.06350.00010.07650.00480.01520.142-0.01940.16248.199725.1519255.1127
160.15830.0421-0.02560.1720.08820.06850.0056-0.0228-0.05220.0202-0.00960.0328-0.00760.02620.02280.0422-0.0016-0.0030.10010.00730.059328.316430.3372264.8183
170.00440.00120.00070.002-0.00260.0062-0.049-0.0522-0.06180.00730.0437-0.04580.1122-0.00310.00210.0915-0.00130.00770.13380.03190.196627.177916.7072265.9162
180.06870.0066-0.07460.053-0.06270.09240.00160.0232-0.0482-0.0436-0.00430.01520.01410.03580.00010.0667-0.0105-0.00530.1341-0.00840.118732.526224.5693258.9405
190.03990.00320.01440.0218-0.03860.11550.0627-0.29930.07370.05420.0945-0.03680.04210.13070.020.0561-0.02150.00310.1964-0.01930.151449.696636.8159268.051
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:7)A2 - 7
2X-RAY DIFFRACTION2(chain A and resid 8:19)A8 - 19
3X-RAY DIFFRACTION3(chain A and resid 20:25)A20 - 25
4X-RAY DIFFRACTION4(chain A and resid 26:29)A26 - 29
5X-RAY DIFFRACTION5(chain A and resid 30:43)A30 - 43
6X-RAY DIFFRACTION6(chain A and resid 44:49)A44 - 49
7X-RAY DIFFRACTION7(chain A and resid 50:58)A50 - 58
8X-RAY DIFFRACTION8(chain A and resid 59:74)A59 - 74
9X-RAY DIFFRACTION9(chain A and resid 75:84)A75 - 84
10X-RAY DIFFRACTION10(chain A and resid 85:102)A85 - 102
11X-RAY DIFFRACTION11(chain A and resid 103:116)A103 - 116
12X-RAY DIFFRACTION12(chain A and resid 117:139)A117 - 139
13X-RAY DIFFRACTION13(chain A and resid 140:157)A140 - 157
14X-RAY DIFFRACTION14(chain A and resid 158:171)A158 - 171
15X-RAY DIFFRACTION15(chain A and resid 172:185)A172 - 185
16X-RAY DIFFRACTION16(chain A and resid 186:240)A186 - 240
17X-RAY DIFFRACTION17(chain A and resid 241:249)A241 - 249
18X-RAY DIFFRACTION18(chain A and resid 250:278)A250 - 278
19X-RAY DIFFRACTION19(chain A and resid 279:301)A279 - 301

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