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- PDB-5igz: Macrolide 2'-phosphotransferase type II - complex with GDP and sp... -

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Basic information

Entry
Database: PDB / ID: 5igz
TitleMacrolide 2'-phosphotransferase type II - complex with GDP and spiramycin
ComponentsMacrolide 2'-phosphotransferase II
KeywordsTRANSFERASE/ANTIBIOTIC / macrolide phosphotransferase / kinase / TRANSFERASE-ANTIBIOTIC complex
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
GUANOSINE-5'-DIPHOSPHATE / SPIRAMYCIN I / Macrolide 2'-phosphotransferase II
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 ...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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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)35,8625
Polymers34,5271
Non-polymers1,3354
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-34 kcal/mol
Surface area13950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.240, 72.430, 77.080
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-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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SPR / SPIRAMYCIN I


Mass: 843.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H74N2O14
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.25 Å3/Da / Density % sol: 45.45 %
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: 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: 1.6→44.9 Å / Num. obs: 41503 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 23.59
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.6-1.640.6753.031100
1.64-1.690.553.71100
1.69-1.740.4274.721100
1.74-1.790.3435.791100
1.79-1.850.2677.461100
1.85-1.910.219.461100
1.91-1.980.15113.011100
1.98-2.070.11117.15199.9
2.07-2.160.09419.81100
2.16-2.260.07325.141100
2.26-2.390.06528.251100
2.39-2.530.05532.45199.9
2.53-2.70.04737.5199.9
2.7-2.920.0443.66199.9
2.92-3.20.03351.31199.9
3.2-3.580.0359.15199.9
3.58-4.130.02763.581100
4.13-5.060.02266.781100
5.06-7.160.02265.181100
7.160.0266.49199.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IGV

5igv


Resolution: 1.6→44.9 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 19.45
RfactorNum. reflection% reflection
Rfree0.1952 2076 5 %
Rwork0.1606 --
obs0.1623 41494 99.93 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Bsol: 57.065 Å2 / ksol: 0.412 e/Å3
Displacement parametersBiso max: 69.04 Å2 / Biso mean: 26.76 Å2 / Biso min: 8.8 Å2
Baniso -1Baniso -2Baniso -3
1--8.2757 Å2-0 Å20 Å2
2---3.3125 Å2-0 Å2
3---11.5883 Å2
Refinement stepCycle: final / Resolution: 1.6→44.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2412 0 175 385 2972
Biso mean--20.45 34.28 -
Num. residues----299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192614
X-RAY DIFFRACTIONf_angle_d1.4793474
X-RAY DIFFRACTIONf_chiral_restr0.082374
X-RAY DIFFRACTIONf_plane_restr0.008443
X-RAY DIFFRACTIONf_dihedral_angle_d14.492934
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5999-1.63720.30111370.259625932730
1.6372-1.67810.25491370.234126002737
1.6781-1.72350.24591360.211925802716
1.7235-1.77420.25621360.194925902726
1.7742-1.83150.21741360.179125822718
1.8315-1.89690.21751380.169826102748
1.8969-1.97290.19491370.166226142751
1.9729-2.06270.22171370.157725982735
2.0627-2.17140.2081360.150825942730
2.1714-2.30750.1811390.143626302769
2.3075-2.48560.18381390.140126342773
2.4856-2.73570.17031380.151226242762
2.7357-3.13150.19251400.147926732813
3.1315-3.9450.17661420.149526872829
3.945-44.91790.18621480.16328092957
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)
12.7948-0.0784-0.84095.0761.34183.264-0.0225-0.21470.05570.24380.1819-0.46810.21810.2909-0.13360.17590.0263-0.0570.2165-0.01220.26712.11431.3831-8.4105
22.1135-0.8929-0.28672.6502-0.03341.5667-0.09190.1513-0.0962-0.09230.1432-0.30150.21450.0048-0.04980.2028-0.032-0.00020.2036-0.02760.18697.31094.4001-16.0221
33.23961.45841.86253.45332.18923.80840.0604-0.2832-0.22260.259-0.11230.26790.1107-0.2430.08210.1703-0.00230.02410.16690.03090.1794-9.11611.771-11.221
41.9802-0.19920.56343.0016-0.29541.362-0.00610.20380.068-0.2739-0.0859-0.05610.00130.13430.07880.1586-0.0130.02090.1968-0.00820.1136-1.70528.5939-20.9921
54.16931.7704-1.32554.9415-1.67843.9436-0.03150.53530.1212-0.63090.06370.26610.0080.0775-0.05570.2815-0.0072-0.0750.28340.00620.183-15.15848.6786-30.8214
61.07590.53470.20733.84532.01981.7701-0.0205-0.1814-0.14820.1996-0.11080.63710.1262-0.19050.10140.1476-0.01880.04440.22110.01240.3688-25.701610.5459-9.2401
71.15880.01820.12081.5910.0771.1362-0.05750.1820.1095-0.2627-0.01870.4758-0.0934-0.12490.05210.1609-0.0072-0.06540.15810.00660.2277-20.164616.5237-21.3774
84.2128-1.3421-0.09745.6866-0.72152.9447-0.1352-0.29040.41960.51750.12910.1814-0.18490.17650.03030.2486-0.01650.01790.196-0.04830.2177-10.10525.3015-4.7899
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:21)A1 - 21
2X-RAY DIFFRACTION2(chain A and resid 22:49)A22 - 49
3X-RAY DIFFRACTION3(chain A and resid 50:74)A50 - 74
4X-RAY DIFFRACTION4(chain A and resid 75:117)A75 - 117
5X-RAY DIFFRACTION5(chain A and resid 118:139)A118 - 139
6X-RAY DIFFRACTION6(chain A and resid 140:169)A140 - 169
7X-RAY DIFFRACTION7(chain A and resid 170:280)A170 - 280
8X-RAY DIFFRACTION8(chain A and resid 281:299)A281 - 299

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