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- PDB-5igw: Macrolide 2'-phosphotransferase type II - complex with GDP and cl... -

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Basic information

Entry
Database: PDB / ID: 5igw
TitleMacrolide 2'-phosphotransferase type II - complex with GDP and clarithromycin
ComponentsMacrolide 2'-phosphotransferase II
KeywordsTRANSFERASE / macrolide phosphotransferase / kinase
Function / homologyAminoglycoside phosphotransferase / Phosphotransferase enzyme family / transferase activity / Protein kinase-like domain superfamily / metal ion binding / CLARITHROMYCIN / GUANOSINE-5'-DIPHOSPHATE / Macrolide 2'-phosphotransferase II
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.096 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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)35,7675
Polymers34,5271
Non-polymers1,2404
Water5,423301
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.173, 81.103, 97.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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) / 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-CTY / CLARITHROMYCIN


Mass: 747.953 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H69NO13 / Comment: antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.36 Å3/Da / Density % sol: 47.84 % / Mosaicity: 0.877 °
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: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 0.9793 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.096→37.447 Å / Num. obs: 18372 / % possible obs: 94.7 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.061 / Χ2: 1.064 / Net I/av σ(I): 28.229 / Net I/σ(I): 12.9 / Num. measured all: 109125
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.1-2.182.50.18164.6
2.18-2.2630.172183.7
2.26-2.373.90.15197.4
2.37-2.495.80.1381100
2.49-2.657.10.1221100
2.65-2.857.10.1011100
2.85-3.147.10.081100
3.14-3.597.10.0631100
3.59-4.527.10.051100
4.52-506.70.041199.8

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Processing

Software
NameVersionClassification
PHENIX1.10pre_2104refinement
SCALEPACKdata scaling
XDSdata reduction
PHENIXphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IGU

5igu


Resolution: 2.096→37.447 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 1790 9.97 %
Rwork0.1669 --
obs0.1731 17949 92.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.096→37.447 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 82 301 2745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072520
X-RAY DIFFRACTIONf_angle_d0.9063441
X-RAY DIFFRACTIONf_dihedral_angle_d13.761449
X-RAY DIFFRACTIONf_chiral_restr0.049381
X-RAY DIFFRACTIONf_plane_restr0.004430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0964-2.15310.3069830.2104761X-RAY DIFFRACTION57
2.1531-2.21640.29311090.2104953X-RAY DIFFRACTION73
2.2164-2.2880.28771290.19271158X-RAY DIFFRACTION89
2.288-2.36970.25491370.17681242X-RAY DIFFRACTION93
2.3697-2.46460.26321370.18951294X-RAY DIFFRACTION98
2.4646-2.57670.26751450.18741297X-RAY DIFFRACTION98
2.5767-2.71260.2411460.18151303X-RAY DIFFRACTION98
2.7126-2.88240.24521430.18571318X-RAY DIFFRACTION98
2.8824-3.10490.2351480.19871325X-RAY DIFFRACTION99
3.1049-3.41720.24191480.16831328X-RAY DIFFRACTION99
3.4172-3.91120.22261510.1491349X-RAY DIFFRACTION100
3.9112-4.92590.19131510.12981372X-RAY DIFFRACTION100
4.9259-37.45260.18841630.15631459X-RAY DIFFRACTION100
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)
10.0635-0.07380.03670.1209-0.08780.0737-0.0446-0.02510.40640.66130.03020.1760.0464-0.161-0.01010.5220.05230.10960.3881-0.05730.2554-10.704111.858651.2394
20.1003-0.0304-0.03720.15050.12890.1088-0.4698-0.0570.22590.6830.1486-0.03650.0583-0.127-0.02090.52370.07640.01270.39910.08540.2226-2.73747.152350.9529
31.03830.34950.38370.9861-0.15220.7089-0.2778-0.01710.06880.245-0.11390.15550.06540.5832-0.22850.27130.10870.09370.32110.0709-0.0267-5.25847.273643.9796
40.0662-0.0388-0.07160.02530.05310.0423-0.0231-0.0097-0.0117-0.051-0.0090.1124-0.02460.0155-00.16090.00370.03350.1888-0.0110.2608-11.67088.595228.8219
50.2438-0.2893-0.09780.4145-0.10720.4725-0.1532-0.2212-0.17420.34760.09880.15070.2070.0613-0.00090.18290.04260.03260.203-0.00030.2097-4.71534.776236.7856
60.3083-0.019-0.16120.23570.02980.0818-0.1806-0.0748-0.09260.03630.01980.13830.04530.0448-0.00870.09240.0302-0.00240.1595-0.00560.17074.8553-3.991625.0937
70.4586-0.2755-0.19520.62440.19110.57230.18630.30380.1123-0.3556-0.18380.1771-0.5885-0.1704-0.02640.4374-0.01390.00720.12680.06220.12144.075316.17569.9476
80.2045-0.06720.03380.025-0.01520.0090.02090.3556-0.1946-0.1367-0.11790.0511-0.0464-0.15340.00110.4659-0.08120.03390.2756-0.02140.14587.86658.36782.6907
90.6118-0.1369-0.28150.67970.31490.2189-0.1383-0.0943-0.0689-0.03560.11660.0801-0.04650.016500.08650.0084-0.01120.12860.00040.12643.39181.489423.4454
100.1702-0.1952-0.00560.2547-0.09150.2391-0.01490.112-0.0812-0.23760.0711-0.14490.00070.1649-0.00010.1492-0.01630.01390.1748-0.02140.17528.8667-3.04312.4343
110.16090.04510.08340.40890.3870.3504-0.492-0.22780.34320.36830.355-0.3918-0.23010.19010.01450.64280.0753-0.1310.2042-0.0440.24028.459820.35123.582
120.0011-0.00120.00190.0406-0.02950.01920.3358-0.17890.2126-0.53960.040.1288-0.2023-0.21940.00290.4866-0.0464-0.13690.33190.00770.58516.685422.264220.0029
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:17)
2X-RAY DIFFRACTION2(chain A and resid 18:28)
3X-RAY DIFFRACTION3(chain A and resid 29:51)
4X-RAY DIFFRACTION4(chain A and resid 52:75)
5X-RAY DIFFRACTION5(chain A and resid 76:108)
6X-RAY DIFFRACTION6(chain A and resid 109:143)
7X-RAY DIFFRACTION7(chain A and resid 144:180)
8X-RAY DIFFRACTION8(chain A and resid 181:190)
9X-RAY DIFFRACTION9(chain A and resid 191:240)
10X-RAY DIFFRACTION10(chain A and resid 241:271)
11X-RAY DIFFRACTION11(chain A and resid 272:289)
12X-RAY DIFFRACTION12(chain A and resid 290:299)

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