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- PDB-5igu: Macrolide 2'-phosphotransferase type II -

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Basic information

Entry
Database: PDB / ID: 5igu
TitleMacrolide 2'-phosphotransferase type II
ComponentsMacrolide 2'-phosphotransferase II
KeywordsTRANSFERASE / macrolide phosphotransferase / kinase
Function / homology: / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / transferase activity / Protein kinase-like domain superfamily / metal ion binding / Macrolide 2'-phosphotransferase II
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 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 1.5Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 II


Theoretical massNumber of molelcules
Total (without water)34,9491
Polymers34,9491
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.360, 114.890, 92.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-426-

HOH

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Components

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


Mass: 34949.262 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.5
Details: 0.15 M calcium acetate, 0.1 M sodium cacodylate pH 6.5, 16% PEG 8000 and 20% glycerol

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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: Jun 29, 2009
RadiationMonochromator: DCM / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→19.897 Å / Num. obs: 18990 / % possible obs: 87.6 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 21.84
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.1-2.150.3672.27169.3
2.15-2.210.273.33177.4
2.21-2.280.325317.3
2.28-2.350.1935.65187.9
2.35-2.420.1787.06199
2.42-2.510.1638.37199
2.51-2.60.12110.35199.7
2.6-2.710.10712.08197.1
2.71-2.830.07115.89199.8
2.83-2.970.0618.35199.9
2.97-3.130.04722.79199.9
3.13-3.320.03428.9199.5
3.32-3.550.02935.75196.5
3.55-3.830.02342.41196.5
3.83-4.20.02247.97195.4
4.2-4.70.0252.34199
4.7-5.420.01952.17198.6
5.42-6.640.0251.85198
6.64-9.390.01658.2197.5
9.390.01559.55185.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→19.897 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 23.86
RfactorNum. reflection% reflection
Rfree0.2214 1910 10.06 %
Rwork0.1983 --
obs0.2006 18978 89.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 132.29 Å2 / Biso mean: 41.28 Å2 / Biso min: 15.65 Å2
Refinement stepCycle: final / Resolution: 2.1→19.897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2085 0 0 109 2194
Biso mean---39.19 -
Num. residues----264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112137
X-RAY DIFFRACTIONf_angle_d1.2982906
X-RAY DIFFRACTIONf_chiral_restr0.079317
X-RAY DIFFRACTIONf_plane_restr0.006372
X-RAY DIFFRACTIONf_dihedral_angle_d15.098760
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 (%)
2.1-2.15250.30291070.2441976108371
2.1525-2.21060.25851130.21191037115078
2.2106-2.27560.2947190.228817219178
2.2756-2.34890.22511340.20781166130093
2.3489-2.43270.22961490.18921361151099
2.4327-2.52990.26031480.203513531501100
2.5299-2.64480.23831550.184913541509100
2.6448-2.78390.23971550.215913581513100
2.7839-2.95780.20021510.195713461497100
2.9578-3.18530.22871530.197113851538100
3.1853-3.50430.21751520.193413701522100
3.5043-4.00780.20731540.18861358151299
4.0078-5.03580.20331580.171813901548100
5.0358-19.89780.22111620.22641442160498
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)
11.77760.35570.1622.05660.61682.0661-0.05840.1713-0.6766-0.33720.0092-0.4411.0068-0.34530.11160.6516-0.10520.10050.35330.10360.534133.14118.258640.3233
21.04330.40330.15540.6923-0.95151.9185-0.15470.4378-0.1978-0.11710.06440.34690.1563-0.93880.26960.4149-0.0490.03040.5593-0.04170.345924.849127.165325.7207
32.84690.11360.51960.88270.00252.6899-0.06680.2154-0.0967-0.03250.0264-0.10670.00780.24280.02150.18090.0076-0.01070.19170.0330.200445.538329.828135.3251
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 32:94)A32 - 94
2X-RAY DIFFRACTION2(chain A and resid 95:121)A95 - 121
3X-RAY DIFFRACTION3(chain A and resid 122:299)A122 - 299

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