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- PDB-7w15: Crystal Structure of MPH-E in complex with GTP and Erythromycin -

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Basic information

Entry
Database: PDB / ID: 7w15
TitleCrystal Structure of MPH-E in complex with GTP and Erythromycin
ComponentsMacrolide 2'-phosphotransferase
KeywordsTRANSFERASE / Antibotic resistance
Function / homologyAminoglycoside phosphotransferase / Phosphotransferase enzyme family / transferase activity / GTP binding / Protein kinase-like domain superfamily / metal ion binding / ERYTHROMYCIN A / GUANOSINE-5'-TRIPHOSPHATE / Macrolide 2'-phosphotransferase
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsQi, Q. / Kuang, L. / Jiang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2019YJ0083 China
CitationJournal: To Be Published
Title: Crystal Structure of the Acinetobacter baumannii Macrolide Phosphotransferases E Reveal the Novel Catalysis Mechanism
Authors: Qi, Q. / Kuang, L. / Jiang, Y.
History
DepositionNov 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.source_name / _pdbx_initial_refinement_model.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Macrolide 2'-phosphotransferase
A: Macrolide 2'-phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,08314
Polymers69,2392
Non-polymers2,84412
Water15,006833
1
B: Macrolide 2'-phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1348
Polymers34,6201
Non-polymers1,5147
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14210 Å2
MethodPISA
2
A: Macrolide 2'-phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9506
Polymers34,6201
Non-polymers1,3305
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-9 kcal/mol
Surface area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.620, 50.278, 97.396
Angle α, β, γ (deg.)90.000, 115.410, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 293 or resid 301 through 302))
d_2ens_1chain "B"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETVALVALAB1 - 2931 - 293
d_12ERYERYERYERYAJ401
d_13GTPGTPGTPGTPAK402
d_21METMETVALVALBA1 - 2931 - 293
d_22ERYERYERYERYBC401
d_23GTPGTPGTPGTPBD402

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Macrolide 2'-phosphotransferase / Macrolide 2'-phosphotransferase / Mph(E)/Mph(G) family / Mph(E) family macrolide 2'- ...Macrolide 2'-phosphotransferase / Mph(E)/Mph(G) family / Mph(E) family macrolide 2'-phosphotransferase / Mph(E) macrolide 2'-phosphotransferase / Mph2 / Putative aminoglycoside phosphotransferase


Mass: 34619.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: mph(E)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A5Y459

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Non-polymers , 5 types, 845 molecules

#2: Chemical ChemComp-ERY / ERYTHROMYCIN A / Erythromycin


Mass: 733.927 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H67NO13 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 833 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.7 Å3/Da / Density % sol: 54.49 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: O.O8 M Mggnesium acetate tetrahydrate; 0.05 M sodium cacodylate pH6.5; 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.973 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 72216 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 19.92 Å2 / CC1/2: 0.988 / Rrim(I) all: 0.107 / Net I/σ(I): 19.7
Reflection shellResolution: 1.77→1.8 Å / Mean I/σ(I) obs: 3 / Num. unique obs: 3600 / CC1/2: 0.872 / Rrim(I) all: 0.517 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→34.85 Å / SU ML: 0.1681 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.1932
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1959 2000 2.79 %
Rwork0.1879 69722 -
obs0.1881 71722 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.23 Å2
Refinement stepCycle: LAST / Resolution: 1.77→34.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4716 0 184 833 5733
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01324994
X-RAY DIFFRACTIONf_angle_d1.35526793
X-RAY DIFFRACTIONf_chiral_restr0.5344782
X-RAY DIFFRACTIONf_plane_restr0.0102831
X-RAY DIFFRACTIONf_dihedral_angle_d16.10241841
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.599001571713 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.820.22511400.22464778X-RAY DIFFRACTION96.17
1.82-1.870.22131380.21834928X-RAY DIFFRACTION98.5
1.87-1.920.22871380.21574904X-RAY DIFFRACTION98.63
1.92-1.980.22571400.21444941X-RAY DIFFRACTION99.22
1.98-2.050.21651450.20344948X-RAY DIFFRACTION99.3
2.05-2.140.22121400.20154947X-RAY DIFFRACTION99.34
2.14-2.230.23291450.20044998X-RAY DIFFRACTION99.73
2.23-2.350.20931460.19914989X-RAY DIFFRACTION99.67
2.35-2.50.23521430.19985021X-RAY DIFFRACTION99.75
2.5-2.690.20351470.19894970X-RAY DIFFRACTION99.69
2.69-2.960.20181390.20325037X-RAY DIFFRACTION99.71
2.96-3.390.1951450.18175030X-RAY DIFFRACTION99.85
3.39-4.270.16481440.16175066X-RAY DIFFRACTION99.96
4.27-34.850.16271500.1645165X-RAY DIFFRACTION99.4
Refinement TLS params.Method: refined / Origin x: -1.93796165461 Å / Origin y: -13.3804685763 Å / Origin z: 24.8057055858 Å
111213212223313233
T0.11292704633 Å20.0187684382607 Å20.0159018797431 Å2-0.122158133222 Å20.00610689847768 Å2--0.101895290704 Å2
L0.12320684668 °2-0.0927177290808 °20.103803961849 °2-0.300846919447 °2-0.00428965379427 °2--0.243328323104 °2
S-0.0272133535351 Å °-0.0319201583533 Å °-0.00716862002008 Å °0.0459676701285 Å °0.0159642603309 Å °0.0315704767651 Å °-0.0250056461972 Å °-0.0475880297584 Å °-7.23908587347E-5 Å °
Refinement TLS groupSelection details: all

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