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- PDB-5lrn: Structure of mono-zinc MCR-1 in P21 space group -

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Basic information

Entry
Database: PDB / ID: 5lrn
TitleStructure of mono-zinc MCR-1 in P21 space group
ComponentsPhosphatidylethanolamine transferase Mcr-1
KeywordsTRANSFERASE / phosphotehanolamine / metalloenzyme / colistin / antibiotic resistance
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, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable phosphatidylethanolamine transferase Mcr-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsHinchliffe, P. / Paterson, N.G. / Spencer, J.
Funding support United Kingdom, China, 4items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/P007295/1 United Kingdom
National Natural Science Foundation of China31530076 China
National Natural Science Foundation of China8161101130 China
National Natural Science Foundation of China31422055 China
CitationJournal: Sci Rep / Year: 2017
Title: Insights into the Mechanistic Basis of Plasmid-Mediated Colistin Resistance from Crystal Structures of the Catalytic Domain of MCR-1.
Authors: Hinchliffe, P. / Yang, Q.E. / Portal, E. / Young, T. / Li, H. / Tooke, C.L. / Carvalho, M.J. / Paterson, N.G. / Brem, J. / Niumsup, P.R. / Tansawai, U. / Lei, L. / Li, M. / Shen, Z. / Wang, ...Authors: Hinchliffe, P. / Yang, Q.E. / Portal, E. / Young, T. / Li, H. / Tooke, C.L. / Carvalho, M.J. / Paterson, N.G. / Brem, J. / Niumsup, P.R. / Tansawai, U. / Lei, L. / Li, M. / Shen, Z. / Wang, Y. / Schofield, C.J. / Mulholland, A.J. / Shen, J. / Fey, N. / Walsh, T.R. / Spencer, J.
History
DepositionAug 19, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphatidylethanolamine transferase Mcr-1
B: Phosphatidylethanolamine transferase Mcr-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9487
Polymers72,5412
Non-polymers4075
Water15,637868
1
A: Phosphatidylethanolamine transferase Mcr-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5204
Polymers36,2701
Non-polymers2503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphatidylethanolamine transferase Mcr-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4283
Polymers36,2701
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.200, 82.330, 81.740
Angle α, β, γ (deg.)90.00, 104.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 36270.484 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 / Plasmid: popinF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): SoluBL21
References: UniProt: A0A0R6L508, Transferases; Transferring phosphorus-containing groups
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 868 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.66 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2 M Lithium chloride, 0.1 M sodium acetate pH 5.0, 20% w/v PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97831 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97831 Å / Relative weight: 1
ReflectionResolution: 1.55→50.56 Å / Num. obs: 94911 / % possible obs: 98 % / Redundancy: 6.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.097 / Net I/σ(I): 9.3
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.519 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LRM

5lrm


Resolution: 1.55→50.556 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.47
RfactorNum. reflection% reflection
Rfree0.1888 4428 4.67 %
Rwork0.1651 --
obs0.1662 94874 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.55→50.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5090 0 20 868 5978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115293
X-RAY DIFFRACTIONf_angle_d1.2277195
X-RAY DIFFRACTIONf_dihedral_angle_d13.6931922
X-RAY DIFFRACTIONf_chiral_restr0.056789
X-RAY DIFFRACTIONf_plane_restr0.006948
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.56760.36491490.33942960X-RAY DIFFRACTION97
1.5676-1.58610.39641570.31962956X-RAY DIFFRACTION96
1.5861-1.60540.32241430.28982956X-RAY DIFFRACTION97
1.6054-1.62570.33411410.28283001X-RAY DIFFRACTION97
1.6257-1.64710.33021510.27882929X-RAY DIFFRACTION96
1.6471-1.66970.30781290.26932988X-RAY DIFFRACTION96
1.6697-1.69350.28561420.25312961X-RAY DIFFRACTION97
1.6935-1.71880.31421510.24892974X-RAY DIFFRACTION97
1.7188-1.74570.24021490.22873018X-RAY DIFFRACTION97
1.7457-1.77430.24611140.22822996X-RAY DIFFRACTION97
1.7743-1.80490.26471600.21852989X-RAY DIFFRACTION97
1.8049-1.83770.20721410.1942974X-RAY DIFFRACTION97
1.8377-1.87310.20491310.17763046X-RAY DIFFRACTION97
1.8731-1.91130.20881530.17152964X-RAY DIFFRACTION98
1.9113-1.95290.20031420.17663028X-RAY DIFFRACTION98
1.9529-1.99830.20381460.17493015X-RAY DIFFRACTION98
1.9983-2.04830.18041480.15322985X-RAY DIFFRACTION98
2.0483-2.10370.19551430.14973054X-RAY DIFFRACTION98
2.1037-2.16560.17221560.14963007X-RAY DIFFRACTION98
2.1656-2.23550.18451510.14463037X-RAY DIFFRACTION98
2.2355-2.31540.17351550.14233033X-RAY DIFFRACTION99
2.3154-2.40810.18441440.15623044X-RAY DIFFRACTION99
2.4081-2.51760.20111580.15553044X-RAY DIFFRACTION99
2.5176-2.65040.1851550.15253041X-RAY DIFFRACTION99
2.6504-2.81640.18521500.15233042X-RAY DIFFRACTION99
2.8164-3.03380.17441500.14933082X-RAY DIFFRACTION99
3.0338-3.33910.17311660.14043040X-RAY DIFFRACTION99
3.3391-3.82210.1311690.13153060X-RAY DIFFRACTION99
3.8221-4.81490.11741500.11823093X-RAY DIFFRACTION98
4.8149-50.58240.15271340.14943129X-RAY DIFFRACTION98
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)
11.0607-1.0126-0.03111.90821.40183.09840.0432-0.0687-0.10040.04030.129-0.12240.16940.3613-0.17790.0893-0.02490.03010.07340.02630.132336.8814-72.923410.1839
22.7787-0.41190.80072.3957-0.03311.92220.0397-0.03-0.1152-0.07730.00560.18280.0542-0.1793-0.03380.0916-0.02710.01910.09450.00310.11388.1009-71.57185.6068
31.0819-0.02140.00240.37470.0571.3264-0.0086-0.14290.00940.0588-0.006-0.0309-0.0026-0.00170.01470.10590.0026-0.00260.0832-0.00260.107128.1701-64.25817.5973
41.8346-0.64781.05560.7654-0.873.0151-0.0489-0.06270.1823-0.0167-0.037-0.0765-0.22080.04960.10650.1078-0.01260.00630.0473-0.01530.144828.5025-54.66165.0166
56.1356-4.5982-0.39864.31040.54081.16880.2820.29370.2401-0.3085-0.2319-0.0795-0.11590.0081-0.0350.1068-0.0150.0140.06060.01540.096322.499-57.4188-4.2989
63.8579-2.05020.45181.6012-0.17580.4647-0.0465-0.02690.20880.01650.012-0.0521-0.0142-0.03650.01290.0901-0.01270.01420.039-0.00070.088817.5148-59.80782.7536
74.4676-1.245-1.41133.01260.6097.6372-0.0052-0.4810.64440.0778-0.04020.1306-0.74060.03930.00060.14-0.00570.01020.1979-0.06090.2273-1.4961-53.02846.6044
81.1528-0.32220.33910.359-0.13780.2962-0.0407-0.1330.03950.03140.01870.04310.0078-0.08970.01760.0939-0.00490.00870.0807-0.00650.11313.4286-65.12755.7511
92.4321-1.6528-2.39194.41724.64567.6886-0.0512-0.2525-0.04610.3427-0.06710.18190.2331-0.34890.12440.11-0.00040.00720.14460.01860.096913.1717-68.25116.5366
104.4697-0.5364-2.60123.60180.7574.3172-0.10820.194-0.3923-0.1051-0.1089-0.01660.4832-0.15070.21440.1390.0049-0.00950.06730.00480.141720.6937-81.74889.0827
113.9141-0.0306-1.09221.46510.89723.3850.0103-0.2847-0.25220.17590.0323-0.0490.35410.1129-0.09520.15230.0112-0.00910.06780.03190.141529.2168-77.052716.1401
122.20810.4576-0.65260.10370.06763.96740.0602-0.00190.071-0.08110.01710.1161-0.2352-0.472-0.08520.13570.0214-0.00520.0652-0.02120.1545-0.6826-62.1957-29.5597
131.75530.16110.40561.7596-0.30171.06890.0957-0.0646-0.21440.07210.0266-0.06830.18570.0626-0.06720.16910.0393-0.02190.0904-0.02980.125918.8421-82.2504-21.3806
141.1013-0.05390.52120.6776-0.12611.8680.00270.1982-0.0161-0.1207-0.0054-0.01960.01860.10530.01730.10550.0128-0.0020.1272-0.01170.09649.8782-66.0055-37.9309
153.6605-0.61653.22340.7678-0.34945.6287-0.13540.24360.2682-0.0241-0.0152-0.0611-0.3550.42540.15210.1501-0.03190.01270.12060.02720.147819.4352-56.8625-29.1815
169.0383-2.3408-0.41261.47690.05641.5076-0.1307-0.28760.42170.10050.1213-0.2138-0.07640.16480.00180.1101-0.0187-0.01150.0947-0.01380.106122.3895-60.2033-18.7403
174.7376-1.85780.18441.17960.04531.31650.07420.2090.1343-0.0237-0.0838-0.11280.0210.1486-0.00340.0874-0.01360.0020.0737-0.01190.093122.6033-67.5708-23.7128
183.5875-0.227-3.51792.74650.41514.01340.08350.4551-0.0043-0.27290.0189-0.55430.16350.5188-0.16520.20570.08820.00870.4172-0.06750.281238.7855-79.5203-26.7236
190.8705-0.32630.33340.51880.00820.88430.07150.2246-0.1246-0.0484-0.0568-0.02590.16090.15790.00310.12630.034-0.00570.1197-0.03570.116220.5196-75.0414-25.9197
203.9639-0.5746-0.49113.28760.60092.9218-0.2139-0.0674-0.37930.1293-0.00510.26310.4791-0.06890.26620.09560.0133-0.04240.0456-0.00840.120711.3249-77.6658-25.486
211.9934-0.8633-0.25193.82950.20312.26760.05160.0225-0.23-0.0525-0.03230.16970.2221-0.0753-0.00380.11530.0009-0.03230.1141-0.02070.13683.5255-76.0519-29.6479
224.6962-2.49291.18564.9397-0.03136.50510.17130.0943-0.2988-0.27320.0170.34310.3369-0.448-0.21320.1031-0.0543-0.02040.1432-0.01870.1644-2.5808-73.4684-33.9287
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 216 through 244 )
2X-RAY DIFFRACTION2chain 'A' and (resid 245 through 274 )
3X-RAY DIFFRACTION3chain 'A' and (resid 275 through 326 )
4X-RAY DIFFRACTION4chain 'A' and (resid 327 through 355 )
5X-RAY DIFFRACTION5chain 'A' and (resid 356 through 379 )
6X-RAY DIFFRACTION6chain 'A' and (resid 380 through 406 )
7X-RAY DIFFRACTION7chain 'A' and (resid 407 through 422 )
8X-RAY DIFFRACTION8chain 'A' and (resid 423 through 480 )
9X-RAY DIFFRACTION9chain 'A' and (resid 481 through 497 )
10X-RAY DIFFRACTION10chain 'A' and (resid 498 through 513 )
11X-RAY DIFFRACTION11chain 'A' and (resid 514 through 540 )
12X-RAY DIFFRACTION12chain 'B' and (resid 216 through 244 )
13X-RAY DIFFRACTION13chain 'B' and (resid 245 through 274 )
14X-RAY DIFFRACTION14chain 'B' and (resid 275 through 326 )
15X-RAY DIFFRACTION15chain 'B' and (resid 327 through 355 )
16X-RAY DIFFRACTION16chain 'B' and (resid 356 through 379 )
17X-RAY DIFFRACTION17chain 'B' and (resid 380 through 406 )
18X-RAY DIFFRACTION18chain 'B' and (resid 407 through 422 )
19X-RAY DIFFRACTION19chain 'B' and (resid 423 through 485 )
20X-RAY DIFFRACTION20chain 'B' and (resid 486 through 501 )
21X-RAY DIFFRACTION21chain 'B' and (resid 502 through 525 )
22X-RAY DIFFRACTION22chain 'B' and (resid 526 through 540 )

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