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- PDB-5igy: Macrolide 2'-phosphotransferase type II - complex with GDP and er... -

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Basic information

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


transferase activity / metal ion binding
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 / Macrolide 2'-phosphotransferase II
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.45 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)35,7444
Polymers34,5271
Non-polymers1,2173
Water9,368520
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.870, 80.520, 97.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 34527.211 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: 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
#4: Chemical ChemComp-ERY / ERYTHROMYCIN A


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


Mass: 18.015 Da / Num. of mol.: 520 / 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: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5 / Details: 0.2 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: Feb 23, 2011
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.45→41.818 Å / Num. obs: 56698 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Net I/σ(I): 25.55
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.45-1.490.7582.85199.9
1.49-1.530.5613.81100
1.53-1.570.4185.15199.9
1.57-1.620.3256.621100
1.62-1.670.2688.181100
1.67-1.730.20310.661100
1.73-1.80.15913.351100
1.8-1.870.1217.411100
1.87-1.960.08623.881100
1.96-2.050.06829.591100
2.05-2.160.05535.95199.9
2.16-2.290.04841.041100
2.29-2.450.04344.571100
2.45-2.650.03848.841100
2.65-2.90.03553.891100
2.9-3.240.03158.621100
3.24-3.740.02962.36199.9
3.74-4.590.02764.71199.9
4.59-6.480.02663.71100
6.480.02861.08198.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5IGW

5igw


Resolution: 1.45→41.818 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 18.3
RfactorNum. reflection% reflection
Rfree0.1958 2835 5 %
Rwork0.1701 --
obs0.1714 56698 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.79 Å2 / Biso mean: 20.84 Å2 / Biso min: 4.7 Å2
Refinement stepCycle: final / Resolution: 1.45→41.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2382 0 159 520 3061
Biso mean--12.33 30.05 -
Num. residues----295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092589
X-RAY DIFFRACTIONf_angle_d1.3023535
X-RAY DIFFRACTIONf_chiral_restr0.064386
X-RAY DIFFRACTIONf_plane_restr0.006444
X-RAY DIFFRACTIONf_dihedral_angle_d14.365936
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.4499-1.47490.26391400.251226602800
1.4749-1.50170.26981380.243726132751
1.5017-1.53060.24551410.222526922833
1.5306-1.56180.23981380.206526102748
1.5618-1.59580.25841430.198827052848
1.5958-1.63290.2351380.1926312769
1.6329-1.67380.23471400.184326602800
1.6738-1.7190.26531410.178426822823
1.719-1.76960.20021400.183626592799
1.7696-1.82670.21751420.179426832825
1.8267-1.8920.22451410.1826862827
1.892-1.96780.24091390.173526572796
1.9678-2.05730.21361420.168626852827
2.0573-2.16580.16431400.157826852825
2.1658-2.30150.18521430.152127102853
2.3015-2.47910.16131420.155227092851
2.4791-2.72860.16741440.159527182862
2.7286-3.12330.21440.16227442888
3.1233-3.93460.16011470.151827792926
3.9346-41.83540.18931520.172228953047
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)
13.2336-0.24850.08031.82480.26442.04090.2253-0.2016-0.7610.24880.005-0.00510.4622-0.048-0.25830.48350.0211-0.22580.22230.01010.34911.5774-10.960151.0584
23.18013.29064.78533.9615.69888.5830.1129-0.28120.00540.5008-0.12120.1622-0.0422-0.1840.0270.3536-0.07110.0220.2524-0.00170.17770.4551-7.43949.5316
30.9951.06430.93383.07242.60343.030.0694-0.147-0.16060.2109-0.1006-0.07710.1533-0.23080.08420.21740.0238-0.06020.1827-0.0350.15755.3438-6.209943.7404
45.89251.0805-1.50252.7407-0.50922.52830.08180.041-0.1968-0.13040.1665-0.3080.1030.2001-0.11440.3917-0.0335-0.11950.1731-0.08850.5098.0469-20.626335.6561
51.1683-0.78712.1475.9173-2.22894.0611-0.0847-0.07-0.3308-0.0107-0.0956-0.30570.56520.21140.1420.28280.0896-0.00970.2449-0.01880.280812.9105-14.896729.5888
60.8555-0.25630.07120.93220.31430.7422-0.01010.07750.1588-0.00970.1678-0.30230.00110.36660.07610.0540.0226-0.04550.1673-0.05780.201310.63070.689727.9872
72.38990.43021.2050.36720.85091.9970.15150.0131-0.37330.14850.059-0.18380.31110.101-0.21910.20290.0862-0.1810.1905-0.09380.341614.1416-10.331738.8434
82.4763-0.54051.38861.35160.78692.0165-0.1199-0.2759-0.13080.28640.09390.07830.1406-0.15330.03040.10640.0157-0.00160.1109-0.00760.0762-2.9083-3.675637.5052
94.6381-2.64890.44054.9360.18744.2394-0.1895-0.369-0.0930.146-0.05540.41110.0818-0.26660.17760.09090.0350.01910.2288-0.03480.1665-16.4769-0.045232.5015
104.3287-1.2875-0.82161.31270.22321.4013-0.05810.10390.37-0.040.0762-0.1413-0.26110.0976-0.02830.067-0.0242-0.02410.0863-0.00080.12172.51624.989721.1842
114.3514-1.14520.54334.1082-1.98223.19740.01080.1545-0.0141-0.18490.1428-0.33150.14550.2381-0.08890.13920.01290.05920.1464-0.05030.11189.2659-9.392712.9674
120.78710.1219-0.0731.2538-0.00551.0247-0.06470.2506-0.3006-0.2027-0.0190.03370.4124-0.1393-0.0080.3512-0.07130.05970.1475-0.09010.1367-1.7982-17.43258.6758
130.2758-0.51620.02971.6829-0.51380.29880.07140.0819-0.3459-0.1341-0.07720.28850.4234-0.2714-0.23310.3495-0.2632-0.04240.2766-0.20880.1651-12.0594-18.11238.0629
143.21791.30011.88842.09421.5261.9264-0.16980.3970.1213-0.4945-0.08930.0534-0.1154-0.14920.13990.2633-0.03150.02770.2681-0.00120.0749-3.7196-4.56183.1017
151.04290.0524-0.00720.7897-0.24961.2556-0.1243-0.02530.14760.04360.0446-0.00280.0256-0.1340.05940.04610.005-0.01470.0719-0.01890.0762-3.1044-1.553324.667
164.26690.5352-0.76251.70040.35451.6445-0.08720.25140.3149-0.1920.09790.2167-0.2018-0.19130.05510.0762-0.0076-0.0450.10810.04270.1449-8.0997.503115.686
175.83722.5916-1.17154.1474-0.85522.63760.06850.48420.2183-0.46060.03780.0905-0.1992-0.2796-0.0510.18150.0004-0.01650.16450.03830.1063-6.24942.42447.6809
180.71450.1477-0.67420.48570.12081.4008-0.1730.1304-0.19870.0368-0.0230.0920.4786-0.2160.10960.1922-0.08280.01920.1353-0.03060.1181-9.0183-12.320616.368
193.9073-2.35571.8433.03881.06233.795-0.2441-0.4073-0.28730.10210.01660.28490.3699-0.34240.15040.32580.00680.0970.19340.0490.3304-9.7853-22.828426.6354
207.46192.84251.47976.4495-2.55434.00640.0668-0.1280.1570.17050.02510.50620.011-0.2205-0.09860.4534-0.29540.21250.5347-0.16050.6225-17.1612-21.456917.8578
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 4:19)A4 - 19
2X-RAY DIFFRACTION2(chain A and resid 20:29)A20 - 29
3X-RAY DIFFRACTION3(chain A and resid 30:51)A30 - 51
4X-RAY DIFFRACTION4(chain A and resid 52:56)A52 - 56
5X-RAY DIFFRACTION5(chain A and resid 57:62)A57 - 62
6X-RAY DIFFRACTION6(chain A and resid 63:81)A63 - 81
7X-RAY DIFFRACTION7(chain A and resid 82:89)A82 - 89
8X-RAY DIFFRACTION8(chain A and resid 90:106)A90 - 106
9X-RAY DIFFRACTION9(chain A and resid 107:118)A107 - 118
10X-RAY DIFFRACTION10(chain A and resid 119:144)A119 - 144
11X-RAY DIFFRACTION11(chain A and resid 145:153)A145 - 153
12X-RAY DIFFRACTION12(chain A and resid 154:168)A154 - 168
13X-RAY DIFFRACTION13(chain A and resid 169:184)A169 - 184
14X-RAY DIFFRACTION14(chain A and resid 185:193)A185 - 193
15X-RAY DIFFRACTION15(chain A and resid 194:240)A194 - 240
16X-RAY DIFFRACTION16(chain A and resid 241:256)A241 - 256
17X-RAY DIFFRACTION17(chain A and resid 257:264)A257 - 264
18X-RAY DIFFRACTION18(chain A and resid 265:280)A265 - 280
19X-RAY DIFFRACTION19(chain A and resid 281:293)A281 - 293
20X-RAY DIFFRACTION20(chain A and resid 294:298)A294 - 298

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