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- PDB-5iwu: Macrolide 2'-phosphotransferase type II complexed with erythromycin -

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Basic information

Entry
Database: PDB / ID: 5iwu
TitleMacrolide 2'-phosphotransferase type II complexed with erythromycin
ComponentsMacrolide 2'-phosphotransferase II
KeywordsTRANSFERASE/ANTIBIOTIC / macrolide phosphotransferase / kinase / TRANSFERASE / 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
ACETATE ION / ERYTHROMYCIN A / Macrolide 2'-phosphotransferase II
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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
DepositionMar 22, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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 / _struct_conn.ptnr2_symmetry

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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)35,4525
Polymers34,5271
Non-polymers9254
Water10,647591
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.160, 81.290, 97.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 595 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CA / CALCIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 591 / 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: 47.26 %
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-225 / Detector: CCD / Date: Feb 23, 2011
RadiationMonochromator: DCM / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.3→41.786 Å / Num. obs: 77516 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / CC1/2: 1 / Rmerge(I) obs: 0.037 / Net I/σ(I): 26.98
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.3-1.330.6041.89181.5
1.33-1.370.552.34191.4
1.37-1.410.4423.22197.2
1.41-1.450.3414.96199.7
1.45-1.50.2647.31100
1.5-1.550.2029.641100
1.55-1.610.15312.581100
1.61-1.680.12515.451100
1.68-1.750.09719.81100
1.75-1.840.07924.081100
1.84-1.940.05832.351100
1.94-2.060.04441.791100
2.06-2.20.03650.291100
2.2-2.370.03355.281100
2.37-2.60.0360.11100
2.6-2.910.02766.331100
2.91-3.360.02372.621100
3.36-4.110.0278.26199.9
4.11-5.810.01979.341100
5.810.01876.33198.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IGU

5igu


Resolution: 1.3→41.786 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 17.3
RfactorNum. reflection% reflection
Rfree0.1709 2000 2.58 %
Rwork0.1583 --
obs0.1587 77513 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.97 Å2 / Biso mean: 20.39 Å2 / Biso min: 7.05 Å2
Refinement stepCycle: final / Resolution: 1.3→41.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2405 0 154 591 3150
Biso mean--14.78 30.29 -
Num. residues----299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062678
X-RAY DIFFRACTIONf_angle_d1.0823657
X-RAY DIFFRACTIONf_chiral_restr0.056398
X-RAY DIFFRACTIONf_plane_restr0.005470
X-RAY DIFFRACTIONf_dihedral_angle_d12.382976
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 (%)
1.2999-1.33250.27221160.26514408452481
1.3325-1.36850.2471320.24084947507991
1.3685-1.40880.22061390.21445273541297
1.4088-1.45420.19091450.185154345579100
1.4542-1.50620.18431440.175754895633100
1.5062-1.56650.17231450.154354725617100
1.5665-1.63780.19361450.143854475592100
1.6378-1.72420.17141450.142555015646100
1.7242-1.83220.18051460.14954905636100
1.8322-1.97360.1721460.145755215667100
1.9736-2.17230.14481470.139455145661100
2.1723-2.48660.17361470.142155695716100
2.4866-3.13260.15371480.160656215769100
3.1326-41.80770.16411550.158858275982100
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)
14.6672.2984-1.66543.0059-0.8012.4294-0.0891-0.4252-0.71650.56790.06380.06960.5425-0.00890.09120.44190.034600.29870.05610.24648.9723-14.538552.3913
21.1813-0.49260.21061.3429-0.01411.1189-0.0714-0.18360.00870.21450.0221-0.02630.0996-0.05660.0260.10560.002-0.00520.1192-0.01780.09347.8712-7.507139.0546
31.5362-0.3319-0.13020.83620.26040.8553-0.00080.01480.11940.0687-0.01270.03690.0145-0.12870.01330.067-0.00070.00780.06170.00530.078-5.96951.810227.2927
41.95950.16980.28021.1958-0.02560.74950.10190.3514-0.1747-0.3332-0.05390.01880.1499-0.0164-0.01640.20.03740.00130.1468-0.01140.0638-4.3433-13.96378.0081
51.0671-0.04860.19860.9932-0.12720.73720.00530.02110.1501-0.03590.0031-0.00660.0011-0.041-0.01090.07130.00290.0160.07940.01330.0875-5.04380.118222.3447
61.05481.1065-0.16812.5994-0.07870.4010.05510.16020.2177-0.1213-0.02020.19210.0096-0.0630.00180.13470.01650.00780.1530.03330.1255-8.2476-0.278810.8102
71.4951-0.1354-0.25832.2043-1.47112.46590.0614-0.1253-0.19920.3153-0.03910.2804-0.1232-0.0505-0.00280.2521-0.02040.02280.13960.00250.1915-11.795-21.668222.6784
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:14)A1 - 14
2X-RAY DIFFRACTION2(chain A and resid 15:95)A15 - 95
3X-RAY DIFFRACTION3(chain A and resid 96:143)A96 - 143
4X-RAY DIFFRACTION4(chain A and resid 144:191)A144 - 191
5X-RAY DIFFRACTION5(chain A and resid 192:252)A192 - 252
6X-RAY DIFFRACTION6(chain A and resid 253:273)A253 - 273
7X-RAY DIFFRACTION7(chain A and resid 274:299)A274 - 299

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