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- PDB-6li6: Crystal structure of MCR-1-S treated by Au(PEt3)Cl -

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Basic information

Entry
Database: PDB / ID: 6li6
TitleCrystal structure of MCR-1-S treated by Au(PEt3)Cl
ComponentsProbable phosphatidylethanolamine transferase Mcr-1
KeywordsTRANSFERASE / MCR-1-S Au(PEt3)Cl / ANTIBIOTIC
Function / homology
Function and homology information


transferase activity, transferring phosphorus-containing groups / Transferases; Transferring phosphorus-containing groups / response to antibiotic / plasma membrane
Similarity search - Function
Phosphoethanolamine transferase, N-terminal / Phosphoethanolamine transferase EptA/EptB / Phosphoethanolamine transferase / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
TRIETHYLPHOSPHANE / : / Probable phosphatidylethanolamine transferase Mcr-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.68 Å
AuthorsZhang, Q. / Wang, M. / Sun, H.
CitationJournal: Nat Commun / Year: 2020
Title: Resensitizing carbapenem- and colistin-resistant bacteria to antibiotics using auranofin.
Authors: Sun, H. / Zhang, Q. / Wang, R. / Wang, H. / Wong, Y.T. / Wang, M. / Hao, Q. / Yan, A. / Kao, R.Y. / Ho, P.L. / Li, H.
History
DepositionDec 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable phosphatidylethanolamine transferase Mcr-1
B: Probable phosphatidylethanolamine transferase Mcr-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6849
Polymers74,4632
Non-polymers1,2217
Water4,306239
1
A: Probable phosphatidylethanolamine transferase Mcr-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9415
Polymers37,2311
Non-polymers7094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-7 kcal/mol
Surface area13070 Å2
MethodPISA
2
B: Probable phosphatidylethanolamine transferase Mcr-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7444
Polymers37,2311
Non-polymers5123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-4 kcal/mol
Surface area13090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.820, 84.750, 81.600
Angle α, β, γ (deg.)90.000, 98.170, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable phosphatidylethanolamine transferase Mcr-1 / Polymyxin resistance protein MCR-1


Mass: 37231.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mcr1, mcr-1, APZ14_31440 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0R6L508, Transferases; Transferring phosphorus-containing groups
#2: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Au / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-3EP / TRIETHYLPHOSPHANE / Triethylphosphine


Mass: 118.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100mM Tris-HNO3, pH 8.0, 32% PEG 3350, 25% Glycerol, 2mM Au(PEt3)Cl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.68→46.35 Å / Num. obs: 71454 / % possible obs: 99.5 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.025 / Rrim(I) all: 0.065 / Net I/σ(I): 16.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.68-1.726.80.80452590.8140.330.8799.3
7.51-106.20.0328430.9990.0130.03499.4

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Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
PHENIX1.15_3459refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.68→46.345 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.46
RfactorNum. reflection% reflection
Rfree0.2101 3589 5.03 %
Rwork0.1789 --
obs0.1805 71344 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 140.28 Å2 / Biso mean: 35.4168 Å2 / Biso min: 13.98 Å2
Refinement stepCycle: final / Resolution: 1.68→46.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5050 0 49 239 5338
Biso mean--67.55 32.49 -
Num. residues----646
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.68-1.70210.24811250.234258999
1.7021-1.72540.31721440.238260499
1.7254-1.75010.24561450.2108253499
1.7501-1.77620.23041280.2064262099
1.7762-1.8040.24081410.2076263399
1.804-1.83350.27681300.2022571100
1.8335-1.86520.25771330.20252625100
1.8652-1.89910.26371460.2226255898
1.8991-1.93560.29361540.2374253297
1.9356-1.97510.20291310.1916259099
1.9751-2.01810.23931360.1882614100
2.0181-2.0650.25411350.2057256899
2.065-2.11670.24191210.2015260599
2.1167-2.17390.21591340.18772617100
2.1739-2.23780.23251270.17962619100
2.2378-2.31010.21511270.1831258698
2.3101-2.39260.23991330.17962612100
2.3926-2.48840.23371480.18222627100
2.4884-2.60170.1951470.18392629100
2.6017-2.73880.22111400.17832608100
2.7388-2.91040.20031410.17862622100
2.9104-3.13510.19991370.1792637100
3.1351-3.45050.20091340.16712615100
3.4505-3.94950.18381490.1635261999
3.9495-4.97510.17681560.14812628100
4.9751-100.20111470.1792693100

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