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- PDB-7w19: Crystal Structure of Acinetobacter baumannii MPH-E -

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Basic information

Entry
Database: PDB / ID: 7w19
TitleCrystal Structure of Acinetobacter baumannii MPH-E
ComponentsMacrolide 2'-phosphotransferase
KeywordsTRANSFERASE / Antibotic resistance
Function / homology
Function and homology information


transferase activity / GTP binding / 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
Macrolide 2'-phosphotransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.0Dec 7, 2022Provider: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,3445
Polymers69,2392
Non-polymers1043
Water7,386410
1
A: Macrolide 2'-phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7244
Polymers34,6201
Non-polymers1043
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-9 kcal/mol
Surface area15040 Å2
MethodPISA
2
B: Macrolide 2'-phosphotransferase


Theoretical massNumber of molelcules
Total (without water)34,6201
Polymers34,6201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.844, 142.172, 92.229
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-660-

HOH

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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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.06 Å3/Da / Density % sol: 40.17 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 0.1M Bis-Tris pH 5.7, 18% PEG 3350 (25% PEG 400 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: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 45164 / % possible obs: 99.4 % / Redundancy: 10 % / Biso Wilson estimate: 23.88 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.154 / Net I/σ(I): 4.61
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID% possible allRrim(I) all
1.88-2.179136570.906199.9
2.17-2.6610106090.997199.10.124
2.66-3.761260480.998199.10.079

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5igj

5igj


Resolution: 1.9→46.11 Å / SU ML: 0.2408 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.8805
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2647 2278 5.04 %
Rwork0.2243 42886 -
obs0.2262 45164 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.78 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4676 0 3 410 5089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514779
X-RAY DIFFRACTIONf_angle_d0.83396474
X-RAY DIFFRACTIONf_chiral_restr0.051736
X-RAY DIFFRACTIONf_plane_restr0.0092823
X-RAY DIFFRACTIONf_dihedral_angle_d5.8948622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.3341470.28162679X-RAY DIFFRACTION99.96
1.94-1.990.29481520.2742641X-RAY DIFFRACTION100
1.99-2.040.31691390.24952653X-RAY DIFFRACTION100
2.04-2.090.29481300.24152661X-RAY DIFFRACTION100
2.09-2.150.2731630.24092632X-RAY DIFFRACTION99.96
2.15-2.220.27171330.22852668X-RAY DIFFRACTION99.89
2.22-2.30.27191550.22962656X-RAY DIFFRACTION99.86
2.3-2.390.30441470.23682664X-RAY DIFFRACTION99.96
2.39-2.50.3061240.23912669X-RAY DIFFRACTION99.86
2.5-2.630.30031340.23482693X-RAY DIFFRACTION99.89
2.63-2.80.26871520.23422663X-RAY DIFFRACTION99.86
2.8-3.020.31871390.23672666X-RAY DIFFRACTION99.26
3.02-3.320.25171550.23152666X-RAY DIFFRACTION99.16
3.32-3.80.25271430.20922703X-RAY DIFFRACTION99.3
3.8-4.790.19731230.18672729X-RAY DIFFRACTION99.2
4.79-46.110.23881420.21742843X-RAY DIFFRACTION99.3
Refinement TLS params.Method: refined / Origin x: 19.8773436183 Å / Origin y: 35.1712995805 Å / Origin z: 10.0631492813 Å
111213212223313233
T0.157737110517 Å20.00871417287448 Å20.00189021201815 Å2-0.172792370627 Å2-0.0131764812955 Å2--0.121354428325 Å2
L0.564393297161 °2-0.452413953125 °20.0674670671167 °2-0.610060832081 °2-0.113903222707 °2--0.202176992315 °2
S0.00870004345373 Å °0.0146981921282 Å °0.0239896394124 Å °-0.00819818056646 Å °0.00855442405862 Å °0.0381254059095 Å °-0.0237332223114 Å °-0.0358821726704 Å °-0.00705534831274 Å °
Refinement TLS groupSelection details: all

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