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- PDB-5igp: Macrolide 2'-phosphotransferase type I - complex with GDP and ery... -

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Basic information

Entry
Database: PDB / ID: 5igp
TitleMacrolide 2'-phosphotransferase type I - complex with GDP and erythromycin
ComponentsMacrolide 2'-phosphotransferase
KeywordsTRANSFERASE/ANTIBIOTIC / macrolide phosphotransferase / kinase / TRANSFERASE-ANTIBIOTIC complex
Function / homology
Function and homology information


transferase activity
Similarity search - Function
: / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ERYTHROMYCIN A / GUANOSINE-5'-DIPHOSPHATE / ISOPROPYL ALCOHOL / Macrolide 2'-phosphotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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

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Assembly

Deposited unit
A: Macrolide 2'-phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5044
Polymers33,2671
Non-polymers1,2373
Water5,170287
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)69,0088
Polymers66,5342
Non-polymers2,4746
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_677x-y+1,-y+2,-z+7/31
Buried area6240 Å2
ΔGint-46 kcal/mol
Surface area26760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.140, 45.140, 247.050
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-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
#3: Chemical ChemComp-ERY / ERYTHROMYCIN A


Mass: 733.927 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H67NO13 / 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.19 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.2 / Details: 0.1 M Na citrate, 27% PEG 4000, 18% isopropanol

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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 3, 2010
RadiationMonochromator: DCM / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.6→41.175 Å / Num. obs: 40026 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 20.19
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.6-1.640.7032.44198.9
1.64-1.690.6433.451100
1.69-1.740.4984.921100
1.74-1.790.4296.131100
1.79-1.850.3627.421100
1.85-1.910.2889.471100
1.91-1.980.22812.161100
1.98-2.070.17715.41100
2.07-2.160.13819.041100
2.16-2.260.11821.991100
2.26-2.390.09825.081100
2.39-2.530.08727.681100
2.53-2.70.07430.651100
2.7-2.920.06135.81100
2.92-3.20.05240.911100
3.2-3.580.04146.21100
3.58-4.130.03651.03199.9
4.13-5.060.03253.521100
5.06-7.160.0351.761100
7.160.02752.76199.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.2data extraction
XDSMar 5, 2012data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IGR

5igr


Resolution: 1.6→41.175 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 16.21
RfactorNum. reflection% reflection
Rfree0.1819 1992 4.98 %
Rwork0.1606 --
obs0.1616 40019 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.99 Å2 / Biso mean: 17.25 Å2 / Biso min: 4.38 Å2
Refinement stepCycle: final / Resolution: 1.6→41.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2334 0 168 287 2789
Biso mean--19.9 25.82 -
Num. residues----300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012532
X-RAY DIFFRACTIONf_angle_d1.3183480
X-RAY DIFFRACTIONf_chiral_restr0.071403
X-RAY DIFFRACTIONf_plane_restr0.007440
X-RAY DIFFRACTIONf_dihedral_angle_d12.806892
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 (%)
1.5999-1.63990.27341380.24162586272499
1.6399-1.68430.26881370.205126782815100
1.6843-1.73380.22641400.18626942834100
1.7338-1.78980.21811420.177726472789100
1.7898-1.85380.19841360.165826562792100
1.8538-1.9280.18941420.158926702812100
1.928-2.01570.18571440.156426922836100
2.0157-2.1220.16451380.144927042842100
2.122-2.25490.15511400.139927322872100
2.2549-2.4290.17061420.139927112853100
2.429-2.67340.16661440.149427092853100
2.6734-3.06020.16581450.161227632908100
3.0602-3.8550.18761490.145728022951100
3.855-41.18860.17791550.176329833138100
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)
11.3272-0.59920.62180.6178-0.781.33360.1625-0.20520.28590.1679-0.0696-0.1623-0.7180.09760.00410.346-0.0095-0.00840.1978-0.01840.217527.822257.4053285.5739
21.27420.488-0.97911.8136-0.832.971-0.2398-0.1278-0.1413-0.02410.0945-0.25490.06780.31230.05830.16820.02430.01080.2541-0.00360.145629.879949.6767277.7957
30.41680.10910.14261.48210.39181.1219-0.0501-0.0350.0211-0.05570.04850.0446-0.163-0.06460.00690.0673-0.0053-0.00720.13570.00810.085421.709544.2888270.2201
40.7178-0.17730.23210.52330.15030.7560.02590.0382-0.0360.0243-0.0301-0.07550.02710.08160.01950.0466-0.0355-0.02080.08960.02960.082134.529131.6382262.8935
50.8891-0.0569-0.20470.93950.23240.8377-0.0082-0.0802-0.13610.01680.02090.02210.11470.03750.00380.0203-0.0361-0.02720.13230.02620.068229.841929.407263.9422
61.730.4668-0.34290.8362-0.1010.28710.1049-0.1771-0.12610.0165-0.0882-0.04370.05310.0403-0.02070.0263-0.0423-0.02020.15030.02980.103438.585828.6639262.9563
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:27)A2 - 27
2X-RAY DIFFRACTION2(chain A and resid 28:61)A28 - 61
3X-RAY DIFFRACTION3(chain A and resid 62:103)A62 - 103
4X-RAY DIFFRACTION4(chain A and resid 104:180)A104 - 180
5X-RAY DIFFRACTION5(chain A and resid 181:244)A181 - 244
6X-RAY DIFFRACTION6(chain A and resid 245:301)A245 - 301

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