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- PDB-7w1a: Crystal Structure of MPH-E in complex with GMP and Azithromycin -

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Basic information

Entry
Database: PDB / ID: 7w1a
TitleCrystal Structure of MPH-E in complex with GMP and Azithromycin
ComponentsMacrolide 2'-phosphotransferase
KeywordsTRANSFERASE / Antibotic resistance
Function / homologyAminoglycoside phosphotransferase / Phosphotransferase enzyme family / transferase activity / GTP binding / Protein kinase-like domain superfamily / metal ion binding / GUANOSINE / AZITHROMYCIN / Macrolide 2'-phosphotransferase
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 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 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)71,3046
Polymers69,2392
Non-polymers2,0644
Water1,24369
1
B: Macrolide 2'-phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6523
Polymers34,6201
Non-polymers1,0322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-5 kcal/mol
Surface area14130 Å2
MethodPISA
2
A: Macrolide 2'-phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6523
Polymers34,6201
Non-polymers1,0322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-5 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.014, 45.852, 89.677
Angle α, β, γ (deg.)90.000, 105.710, 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

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Components

#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(DE3) (bacteria) / References: UniProt: A5Y459
#2: Chemical ChemComp-GMP / GUANOSINE / Guanosine


Mass: 283.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZIT / AZITHROMYCIN / Azithromycin


Mass: 748.984 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C38H72N2O12 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antibiotic*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
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: 2.32 Å3/Da / Density % sol: 46.88 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Ammonium acetate, 0.01M Mggnesium acetate tetrahydrate, 0.05M sodium cacodylate pH6.5, 30% PEG 8000 (20% Glycerol as cryoprotectant)

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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: 2.17→50 Å / Num. obs: 33719 / % possible obs: 99.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 44.8 Å2 / CC1/2: 0.986 / Rrim(I) all: 0.082 / Net I/σ(I): 18
Reflection shellResolution: 2.17→2.21 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1617 / CC1/2: 0.621 / Rrim(I) all: 0.71 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5igj

5igj


Resolution: 2.17→40.49 Å / SU ML: 0.356 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.5192
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2831 2000 5.95 %
Rwork0.2541 31640 -
obs0.2559 33640 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.02 Å2
Refinement stepCycle: LAST / Resolution: 2.17→40.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4623 0 144 69 4836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01744866
X-RAY DIFFRACTIONf_angle_d1.62776607
X-RAY DIFFRACTIONf_chiral_restr0.552764
X-RAY DIFFRACTIONf_plane_restr0.0207810
X-RAY DIFFRACTIONf_dihedral_angle_d19.53661773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.220.34791360.3162140X-RAY DIFFRACTION95.27
2.22-2.280.38571400.31462239X-RAY DIFFRACTION98.31
2.28-2.350.36071420.30692236X-RAY DIFFRACTION99.08
2.35-2.430.35041410.29022236X-RAY DIFFRACTION98.96
2.43-2.510.33151430.30622262X-RAY DIFFRACTION99.13
2.51-2.620.34071410.30282220X-RAY DIFFRACTION99.29
2.62-2.730.38081430.30592277X-RAY DIFFRACTION99.34
2.73-2.880.35021440.30442273X-RAY DIFFRACTION99.59
2.88-3.060.33251440.27632281X-RAY DIFFRACTION99.75
3.06-3.290.26921430.28342255X-RAY DIFFRACTION99.54
3.29-3.630.29071430.26052271X-RAY DIFFRACTION99.67
3.63-4.150.28451450.23532297X-RAY DIFFRACTION99.63
4.15-5.230.23061460.21672306X-RAY DIFFRACTION99.72
5.23-40.490.2231490.21192347X-RAY DIFFRACTION97.69
Refinement TLS params.Method: refined / Origin x: -9.82939381833 Å / Origin y: -8.84126055631 Å / Origin z: 22.4310774014 Å
111213212223313233
T0.300270961508 Å20.0821879128295 Å20.0106891010335 Å2-0.338489649642 Å20.0193058705945 Å2--0.313434600058 Å2
L0.771100937665 °20.195578533099 °20.00896893105415 °2-0.456610845376 °20.1936595744 °2--1.14603755356 °2
S0.019556263552 Å °-0.288571816659 Å °-0.0476641328488 Å °0.0922449814168 Å °-0.146383089543 Å °0.0641640657228 Å °-0.0319630490757 Å °-0.189900255904 Å °-0.167271002856 Å °
Refinement TLS groupSelection details: all

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