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- PDB-5lrm: Structure of di-zinc MCR-1 in P41212 space group -

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Basic information

Entry
Database: PDB / ID: 5lrm
TitleStructure of di-zinc MCR-1 in P41212 space group
Componentsphosphatidylethanolamine transferase Mcr-1
KeywordsTRANSFERASE / phosphoethanolamine / colistin / metalloenzyme / zinc
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: 1.75 Å
AuthorsHinchliffe, P. / Spencer, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/P007295/1 United Kingdom
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 1.4May 1, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: phosphatidylethanolamine transferase Mcr-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5065
Polymers36,1911
Non-polymers3154
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-31 kcal/mol
Surface area13120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.044, 49.044, 244.253
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 36190.504 Da / Num. of mol.: 1
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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.03 Å3/Da / Density % sol: 39.39 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M MOPS/HEPES-Na pH 7.5, 10% w/v PEG 20000, 20% v/v PEG MME 550, 0.02 M 1,6-hexanediol, 0.02 M 1-butanol, 0.02 M 1,2-propanediol, 0.02 M 2-propanol, 0.02 M 1,4-butanediol, 0.02 M 1,3-propanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97833 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97833 Å / Relative weight: 1
ReflectionResolution: 1.75→48.85 Å / Num. obs: 34217 / % possible obs: 100 % / Redundancy: 15.5 % / Rmerge(I) obs: 0.029 / Net I/σ(I): 15.1
Reflection shellResolution: 1.75→1.79 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.925 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Initial model built from phases calculated from Zn-SAD datasets

Resolution: 1.75→48.085 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.54
RfactorNum. reflection% reflection
Rfree0.198 1572 5.02 %
Rwork0.1688 --
obs0.1702 31329 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→48.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2447 0 14 155 2616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112518
X-RAY DIFFRACTIONf_angle_d1.1633417
X-RAY DIFFRACTIONf_dihedral_angle_d13.78906
X-RAY DIFFRACTIONf_chiral_restr0.071379
X-RAY DIFFRACTIONf_plane_restr0.005446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7501-1.80650.311650.25952587X-RAY DIFFRACTION100
1.8065-1.87110.26631330.22092641X-RAY DIFFRACTION100
1.8711-1.9460.26571500.19092631X-RAY DIFFRACTION99
1.946-2.03460.24151400.18232654X-RAY DIFFRACTION99
2.0346-2.14190.26871440.17882652X-RAY DIFFRACTION100
2.1419-2.27610.21571370.17482660X-RAY DIFFRACTION100
2.2761-2.45180.19631180.17782730X-RAY DIFFRACTION100
2.4518-2.69850.21531410.18262684X-RAY DIFFRACTION100
2.6985-3.08890.19361450.18532740X-RAY DIFFRACTION100
3.0889-3.89150.20511360.16152797X-RAY DIFFRACTION100
3.8915-48.10270.16091630.15012981X-RAY DIFFRACTION100
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)
10.6672-0.8488-0.13811.88730.29031.86420.1298-0.06450.06560.0047-0.0895-0.05040.0507-0.1137-0.02630.2401-0.0414-0.00510.3428-0.00880.2779-19.372311.680815.0005
21.0542-0.61880.33892.5232-0.18881.87050.0667-0.08160.23890.1004-0.13-0.3986-0.20020.17420.05940.265-0.0647-0.00780.3457-0.00480.3796-9.855720.752113.7292
33.8266-0.6738-0.67482.8126-0.42745.67680.05170.12270.14580.23610.24680.5069-0.7159-0.948-0.35490.48440.1140.08090.4656-0.01910.4067-31.638632.556317.7679
40.9920.1207-0.02490.845-0.14882.10330.1024-0.13730.11920.0921-0.08790.077-0.1089-0.2343-0.02360.2710.0117-0.01250.3579-0.02710.3113-24.386520.026715.6619
51.5168-0.30990.04941.90770.1172.67310.1040.0589-0.18660.0022-0.2270.19230.2996-0.55820.14440.2873-0.046-0.01340.3783-0.01670.3222-24.21548.203718.0188
63.638-1.0025-0.1761.5007-0.43653.01340.0922-0.1489-0.1883-0.0565-0.0831-0.04880.58760.1421-0.02030.3305-0.0046-0.04360.31340.01290.3173-12.99011.491315.322
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 218 through 292 )
2X-RAY DIFFRACTION2chain 'A' and (resid 293 through 397 )
3X-RAY DIFFRACTION3chain 'A' and (resid 398 through 424 )
4X-RAY DIFFRACTION4chain 'A' and (resid 425 through 480 )
5X-RAY DIFFRACTION5chain 'A' and (resid 481 through 513 )
6X-RAY DIFFRACTION6chain 'A' and (resid 514 through 540 )

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