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- PDB-7yjp: Crystal structure of MCR-1 treated by AuCl -

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Basic information

Entry
Database: PDB / ID: 7yjp
TitleCrystal structure of MCR-1 treated by AuCl
ComponentsProbable phosphatidylethanolamine transferase Mcr-1
KeywordsTRANSFERASE / MCR-1-S / AuCl / 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
: / Probable phosphatidylethanolamine transferase Mcr-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.88 Å
AuthorsZhang, Q. / Wang, M. / Sun, H.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)R7070-18 Hong Kong
CitationJournal: J.Biol.Inorg.Chem. / Year: 2023
Title: Gold drugs as colistin adjuvants in the fight against MCR-1 producing bacteria.
Authors: Zhang, Q. / Wang, M. / Hu, X. / Yan, A. / Ho, P.L. / Li, H. / Sun, H.
History
DepositionJul 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)74,8574
Polymers74,4632
Non-polymers3942
Water1,36976
1
A: Probable phosphatidylethanolamine transferase Mcr-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4282
Polymers37,2311
Non-polymers1971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable phosphatidylethanolamine transferase Mcr-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4282
Polymers37,2311
Non-polymers1971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.110, 83.540, 81.900
Angle α, β, γ (deg.)90.000, 99.240, 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.: 2 / Source method: obtained synthetically / Formula: Au / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.14 Å3/Da / Density % sol: 42.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100mM Tris-HNO3, pH 8.0, 32% PEG 3350, 25% Glycerol, 5mM AuCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.88→58.093 Å / Num. obs: 48894 / % possible obs: 96.1 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.038 / Rrim(I) all: 0.07 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.88-1.933.50.67736500.8530.420.79997.9
7.41-9.093.30.0325830.9930.0210.03897

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Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
PHENIXdev_3339refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.88→58.093 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2445 2394 4.92 %
Rwork0.202 46313 -
obs0.2041 48707 95.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.2 Å2 / Biso mean: 41.2595 Å2 / Biso min: 21.98 Å2
Refinement stepCycle: final / Resolution: 1.88→58.093 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5068 0 2 76 5146
Biso mean--60.57 37.45 -
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 (%)
1.88-1.91840.34171320.2791275197
1.9184-1.96010.3111370.2719277697
1.9601-2.00570.34111380.2704273797
2.0057-2.05590.41341470.3684265793
2.0559-2.11140.34881400.2634272997
2.1114-2.17360.25831430.2417266594
2.1736-2.24370.31751560.2358278797
2.2437-2.32390.31671240.2544276697
2.3239-2.4170.41211310.3503234683
2.417-2.5270.28921480.2361279598
2.527-2.66020.30421660.2315276697
2.6602-2.82690.2611240.2315278898
2.8269-3.04510.27661110.2293273095
3.0451-3.35150.23691260.2127274195
3.3515-3.83640.23921680.1825274297
3.8364-4.83310.16361510.1396277997
4.8331-58.090.18061520.1466275895

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