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- PDB-5gov: Crystal Structure of MCR-1, a phosphoethanolamine transferase, ex... -

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Basic information

Entry
Database: PDB / ID: 5gov
TitleCrystal Structure of MCR-1, a phosphoethanolamine transferase, extracellular domain
ComponentsProbable phosphatidylethanolamine transferase Mcr-1
KeywordsTRANSFERASE / MCR-1 / pEtN transferase / zinc-binding / phosphorylation / colistin
Function / homology
Function and homology information


phosphotransferase activity, phosphate group as acceptor / Transferases; Transferring phosphorus-containing groups / 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, 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: 2.33 Å
AuthorsHu, M. / Guo, J. / Chen, S. / Hao, Q.
CitationJournal: Sci Rep / Year: 2016
Title: Crystal Structure of Escherichia coli originated MCR-1, a phosphoethanolamine transferase for Colistin Resistance.
Authors: Hu, M. / Guo, J. / Cheng, Q. / Yang, Z. / Chan, E.W.C. / Chen, S. / Hao, Q.
History
DepositionJul 29, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Advisory / Database references / Category: citation / pdbx_unobs_or_zero_occ_atoms / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 8, 2023Group: 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 / struct_conn_type
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Probable phosphatidylethanolamine transferase Mcr-1
A: Probable phosphatidylethanolamine transferase Mcr-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,12413
Polymers81,4052
Non-polymers71911
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-267 kcal/mol
Surface area25880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.439, 55.833, 219.388
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: 40702.477 Da / Num. of mol.: 2 / Fragment: UNP residues 200-541
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: SHP45 / Gene: mcr1, mcr-1 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0R6L508, Transferases; Transferring phosphorus-containing groups
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.05 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG8000, Sodium cacodylate trihydrate, Zinc acetate dihydrate
PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 29251 / % possible obs: 97.5 % / Redundancy: 11.5 % / Rsym value: 0.104 / Net I/σ(I): 22.27

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KAY

4kay


Resolution: 2.33→39.127 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24
RfactorNum. reflection% reflection
Rfree0.2358 1244 4.68 %
Rwork0.186 --
obs0.1883 26560 89.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.33→39.127 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5029 0 11 193 5233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095147
X-RAY DIFFRACTIONf_angle_d1.1846996
X-RAY DIFFRACTIONf_dihedral_angle_d14.4263075
X-RAY DIFFRACTIONf_chiral_restr0.065775
X-RAY DIFFRACTIONf_plane_restr0.007913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3258-2.41890.3284930.22952030X-RAY DIFFRACTION66
2.4189-2.5290.29211180.22482310X-RAY DIFFRACTION75
2.529-2.66230.27631510.21972479X-RAY DIFFRACTION81
2.6623-2.82910.27871300.22362768X-RAY DIFFRACTION89
2.8291-3.04740.25131260.2072963X-RAY DIFFRACTION95
3.0474-3.35390.23781380.19223094X-RAY DIFFRACTION99
3.3539-3.83890.21891700.16853136X-RAY DIFFRACTION100
3.8389-4.83520.19331560.14853193X-RAY DIFFRACTION100
4.8352-39.13210.22841620.18683343X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 24.5312 Å / Origin y: -14.8497 Å / Origin z: -27.1472 Å
111213212223313233
T0.1904 Å20.0596 Å2-0.0392 Å2-0.2223 Å2-0.0124 Å2--0.1806 Å2
L0.7289 °20.1038 °2-0.7675 °2-0.474 °20.5784 °2--1.4285 °2
S0.0729 Å °-0.045 Å °0.1075 Å °-0.0459 Å °0.0182 Å °-0.0024 Å °-0.1298 Å °0.0048 Å °-0.0726 Å °
Refinement TLS groupSelection details: all

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