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- PDB-5yle: MCR-1 complex with ethanolamine (ETA) -

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Basic information

Entry
Database: PDB / ID: 5yle
TitleMCR-1 complex with ethanolamine (ETA)
ComponentsProbable phosphatidylethanolamine transferase Mcr-1
KeywordsTRANSFERASE / Phosphoethanolamine Transferase / plasmid-mediated transferable colistin resistance gene
Function / homology
Function and homology information


transferase activity, transferring phosphorus-containing groups / Transferases; Transferring phosphorus-containing groups / sulfuric ester hydrolase activity / 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
ETHANOLAMINE / Probable phosphatidylethanolamine transferase Mcr-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWei, P.C. / Song, G.J. / Shi, M.Y. / Zhou, Y.F. / Liu, Y. / Lei, J. / Chen, P. / Yin, L.
Funding support China, 3items
OrganizationGrant numberCountry
National Basic Research Program of China2014CB910103 China
National Natural Science Foundation of China31470738 China
National Thousand (Young) Talents Program China
CitationJournal: FASEB J. / Year: 2018
Title: Substrate analog interaction with MCR-1 offers insight into the rising threat of the plasmid-mediated transferable colistin resistance.
Authors: Wei, P. / Song, G. / Shi, M. / Zhou, Y. / Liu, Y. / Lei, J. / Chen, P. / Yin, L.
History
DepositionOct 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.2Mar 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _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_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_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
Revision 2.1Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6553
Polymers37,5291
Non-polymers1262
Water9,890549
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-7 kcal/mol
Surface area14210 Å2
Unit cell
Length a, b, c (Å)51.860, 73.270, 82.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 37528.840 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 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0R6L508, Transferases; Transferring phosphorus-containing groups
#2: Chemical ChemComp-ETA / ETHANOLAMINE / Ethanolamine


Type: L-peptide COOH carboxy terminus / Mass: 61.083 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H7NO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 549 / 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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 10% (v/v) PEG 1000, 5% (v/v) PEG 8000

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.85→37.69 Å / Num. obs: 27304 / % possible obs: 99 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.0718 / Net I/σ(I): 7.55
Reflection shellResolution: 1.85→1.916 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.3726 / Mean I/σ(I) obs: 2.44 / Num. unique obs: 2662 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NT0
Resolution: 1.85→37.69 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.25
RfactorNum. reflection% reflection
Rfree0.2051 2000 7.33 %
Rwork0.1594 --
obs0.1627 27297 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→37.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2604 0 5 549 3158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032870
X-RAY DIFFRACTIONf_angle_d0.6213935
X-RAY DIFFRACTIONf_dihedral_angle_d14.9811731
X-RAY DIFFRACTIONf_chiral_restr0.044428
X-RAY DIFFRACTIONf_plane_restr0.003528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.89630.2691390.21181751X-RAY DIFFRACTION99
1.8963-1.94760.26621390.19911762X-RAY DIFFRACTION98
1.9476-2.00490.28121410.18381782X-RAY DIFFRACTION99
2.0049-2.06960.22431410.17731797X-RAY DIFFRACTION99
2.0696-2.14360.19691430.16871799X-RAY DIFFRACTION99
2.1436-2.22940.19681420.1591783X-RAY DIFFRACTION99
2.2294-2.33080.21561410.15861789X-RAY DIFFRACTION100
2.3308-2.45370.24321420.1661804X-RAY DIFFRACTION99
2.4537-2.60740.20481430.17141800X-RAY DIFFRACTION99
2.6074-2.80870.24411430.1651815X-RAY DIFFRACTION99
2.8087-3.09130.21181420.14491798X-RAY DIFFRACTION98
3.0913-3.53850.15761430.13971815X-RAY DIFFRACTION99
3.5385-4.45740.15851470.12971852X-RAY DIFFRACTION99
4.4574-43.96470.19541540.16621950X-RAY DIFFRACTION99

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