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- PDB-7waa: Crystal structure of MCR-1-S treated by AgNO3 -

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Basic information

Entry
Database: PDB / ID: 7waa
TitleCrystal structure of MCR-1-S treated by AgNO3
ComponentsProbable phosphatidylethanolamine transferase Mcr-1
KeywordsTRANSFERASE / MCR-1-S AgNO3 / ANTIBIOTIC
Function / homology
Function and homology information


lipid A phosphoethanolamine transferase / phosphotransferase activity, phosphate group as acceptor / lipopolysaccharide core region biosynthetic process / 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
SILVER ION / Phosphatidylethanolamine transferase Mcr-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.58 Å
AuthorsZhang, Q. / Wang, M. / Sun, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Re-sensitization of mcr carrying multidrug resistant bacteria to colistin by silver.
Authors: Zhang, Q. / Wang, R. / Wang, M. / Liu, C. / Koohi-Moghadam, M. / Wang, H. / Ho, P.L. / Li, H. / Sun, H.
History
DepositionDec 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)76,51221
Polymers74,4632
Non-polymers2,04919
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-50 kcal/mol
Surface area25610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.200, 84.420, 81.760
Angle α, β, γ (deg.)90.000, 98.670, 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-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100mM Tris-HNO3, 32% PEG 3350, 25% Glycerol, pH 7.5, 1mM AgNO3, in the prevention of light

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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: Aug 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.58→42.21 Å / Num. obs: 85652 / % possible obs: 98.8 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.026 / Rrim(I) all: 0.068 / Net I/σ(I): 13.8 / Num. measured all: 580725 / Scaling rejects: 111
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.58-1.626.90.7794394063600.810.3190.8442.399.4
7.07-42.216.30.068629410030.9750.0330.07625.198.3

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Processing

Software
NameVersionClassification
Aimless0.6.2data scaling
PHENIX1.14_3219refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.58→42.21 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2125 4338 5.07 %
Rwork0.1931 81277 -
obs0.1941 85615 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.23 Å2 / Biso mean: 37.5384 Å2 / Biso min: 20.79 Å2
Refinement stepCycle: final / Resolution: 1.58→42.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5027 0 19 96 5142
Biso mean--45.74 36.95 -
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 (%)
1.58-1.5980.33811340.27642746100
1.598-1.61680.2631400.2632270999
1.6168-1.63650.24121290.2582271599
1.6365-1.65720.271280.2463271999
1.6572-1.6790.23881280.2364273199
1.679-1.7020.25351580.2393270799
1.702-1.72630.25821540.2292263398
1.7263-1.75210.28111510.2238269098
1.7521-1.77950.25981490.2205255895
1.7795-1.80860.24851460.2196269098
1.8086-1.83980.2491440.21982721100
1.8398-1.87330.24581430.2182746100
1.8733-1.90930.21411730.20782684100
1.9093-1.94830.25151520.20582723100
1.9483-1.99060.21041360.20992735100
1.9906-2.0370.19951360.19952743100
2.037-2.08790.25211420.2108271499
2.0879-2.14430.23641280.2112798100
2.1443-2.20740.22511440.2113266999
2.2074-2.27870.20441540.2271299
2.2787-2.36010.19611310.195274899
2.3601-2.45460.23381410.2143263797
2.4546-2.56630.24041410.2115260895
2.5663-2.70160.26491300.21972747100
2.7016-2.87080.24391490.21452756100
2.8708-3.09240.20081690.22709100
3.0924-3.40350.20021430.1961276699
3.4035-3.89570.22321560.1721272099
3.8957-4.9070.1651360.1437266396
4.907-100.18451730.1717278099
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4101-0.3080.43512.9275-1.48981.92410.07120.01840.3403-0.20240.07850.3891-0.2033-0.1533-0.13590.33230.0016-0.01720.2088-0.01830.3266-4.42114.29343.0904
21.5565-0.55060.31952.36630.6681.88730.01840.1539-0.0794-0.09910.0278-0.0020.12970.1577-0.04370.2811-0.0075-0.00340.2542-0.03080.25379.3049-6.25193.8382
35.944-1.7498-1.02193.10970.50812.6290.01980.25020.6112-0.30810.0671-0.4812-0.38240.4159-0.08850.4331-0.1044-0.01090.30420.05890.394710.811616.72320.6493
41.5925-0.5530.29762.4070.03782.0737-0.1522-0.17110.19260.17120.094-0.1653-0.26220.17530.04110.2919-0.015-0.01640.2594-0.02880.28477.310910.864317.0767
55.6475-2.72251.04822.8868-0.81681.7418-0.334-0.68520.20320.36210.304-0.0173-0.0124-0.2164-0.00790.3044-0.00040.01980.329-0.01910.24893.9261.20723.0114
63.5581-2.35621.46373.4412-0.7222.312-0.0885-0.1190.07910.17410.1509-0.03470.1010.009-0.09350.2724-0.0258-0.00340.2169-0.00890.24048.6621-1.705716.0916
73.37070.7497-0.81013.3882-0.21723.87050.0287-0.372-0.4510.28920.289-0.40960.43820.7699-0.19320.46660.1527-0.0750.43-0.03510.464822.7222-16.194516.5369
83.0721-0.4454-0.07361.942-0.01222.358-0.01330.1886-0.0575-0.02950.0845-0.01560.18390.1443-0.07380.2623-0.0299-0.03690.1883-0.0260.2268.6209-4.98137.3101
92.8194-1.3977-0.88813.29230.87932.00040.15230.52530.0947-0.6361-0.17380.2785-0.2022-0.05690.03710.3745-0.0022-0.06840.30440.0490.26350.46635.9238-5.2986
101.7449-0.0117-0.10871.57220.18850.74730.121-0.4486-0.40350.3416-0.24850.40340.3516-0.58510.09330.4171-0.20090.0420.6003-0.04580.4305-8.992714.710548.7306
111.36391.1197-0.03841.83750.16852.37540.0495-0.07390.1309-0.1258-0.07730.1075-0.04480.040.01840.30750.02380.00880.308-0.0690.29795.748224.546130.8136
123.00520.0263-1.0132.20630.05882.2994-0.033-0.22480.248-0.1359-0.29250.4628-0.1541-0.69060.30160.28030.0082-0.01250.5605-0.23190.4821-15.908925.393639.9219
133.29491.28460.08191.55780.52520.76310.1944-0.6560.50260.3468-0.38060.3517-0.1445-0.46920.09320.3111-0.04080.040.5274-0.17670.33551.684832.687849.7075
143.31511.9022-0.24033.6711-0.7233.26360.1969-0.2080.27850.3115-0.11150.1329-0.17-0.1468-0.09320.2679-0.01430.00020.3094-0.10760.31616.80531.426642.353
156.22761.64941.49152.8131.05554.4006-0.2270.64730.9942-0.8632-0.01420.3011-0.76280.52060.24080.5244-0.16350.00740.50950.05540.468916.282541.91126.7603
163.53341.53240.73342.10830.67121.81250.0505-0.01780.1326-0.1024-0.1140.021-0.08350.01810.07180.23210.02770.03510.2564-0.07830.26015.991426.256234.3468
171.9991-0.36280.10061.6847-0.343.44690.1503-0.0698-0.28120.1005-0.25230.37330.388-0.49820.12940.3421-0.07020.01170.3747-0.10570.4357-6.536713.019736.3768
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 29 )A3 - 29
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 77 )A30 - 77
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 102 )A78 - 102
4X-RAY DIFFRACTION4chain 'A' and (resid 103 through 140 )A103 - 140
5X-RAY DIFFRACTION5chain 'A' and (resid 141 through 164 )A141 - 164
6X-RAY DIFFRACTION6chain 'A' and (resid 165 through 191 )A165 - 191
7X-RAY DIFFRACTION7chain 'A' and (resid 192 through 207 )A192 - 207
8X-RAY DIFFRACTION8chain 'A' and (resid 208 through 286 )A208 - 286
9X-RAY DIFFRACTION9chain 'A' and (resid 287 through 325 )A287 - 325
10X-RAY DIFFRACTION10chain 'B' and (resid 3 through 29 )B3 - 29
11X-RAY DIFFRACTION11chain 'B' and (resid 30 through 76 )B30 - 76
12X-RAY DIFFRACTION12chain 'B' and (resid 77 through 102 )B77 - 102
13X-RAY DIFFRACTION13chain 'B' and (resid 103 through 163 )B103 - 163
14X-RAY DIFFRACTION14chain 'B' and (resid 164 through 191 )B164 - 191
15X-RAY DIFFRACTION15chain 'B' and (resid 192 through 207 )B192 - 207
16X-RAY DIFFRACTION16chain 'B' and (resid 208 through 286 )B208 - 286
17X-RAY DIFFRACTION17chain 'B' and (resid 287 through 325 )B287 - 325

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