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- PDB-5grr: Crystal structure of MCR-1 -

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Basic information

Entry
Database: PDB / ID: 5grr
TitleCrystal structure of MCR-1
ComponentsProbable phosphatidylethanolamine transferase Mcr-1
KeywordsTRANSFERASE / antibiotic resistant / colistin / superbug / phosphoenthanolamine transferase / MCR-1
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 / SAD / molecular replacement / Resolution: 1.45 Å
AuthorsMa, G. / Zhu, Y. / Yu, Z. / Zhang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670753 China
CitationJournal: Sci Rep / Year: 2016
Title: High resolution crystal structure of the catalytic domain of MCR-1
Authors: Ma, G. / Zhu, Y. / Yu, Z. / Ahmad, A. / Zhang, H.
History
DepositionAug 12, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 4, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 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
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_alt_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.ptnr1_symmetry / _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_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_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_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_symmetry

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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)36,5616
Polymers36,1801
Non-polymers3805
Water8,863492
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-39 kcal/mol
Surface area13550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.314, 62.696, 104.831
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 36180.469 Da / Num. of mol.: 1 / Fragment: UNP residues 219-541
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mcr1, mcr-1 / Plasmid: pRHSUL2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)plysS
References: UniProt: A0A0R6L508, Transferases; Transferring phosphorus-containing groups
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / 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.: 492 / 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: 2.12 Å3/Da / Density % sol: 42.08 % / Mosaicity: 0.763 ° / Mosaicity esd: 0.009 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 100 mM Tris-HCl, 20% (v/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.91 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 55886 / % possible obs: 100 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.03 / Rrim(I) all: 0.084 / Χ2: 0.941 / Net I/σ(I): 9.2 / Num. measured all: 434239
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.45-1.57.90.80954900.8420.3050.8660.852100
1.5-1.567.90.58355160.9040.220.6240.86100
1.56-1.637.80.43655410.9390.1650.4670.875100
1.63-1.727.80.31555080.9650.120.3380.869100
1.72-1.837.80.21655430.9810.0820.2310.887100
1.83-1.977.80.14655460.990.0560.1571.029100
1.97-2.177.70.11455720.9910.0440.1221.241100
2.17-2.487.50.08256080.9950.0320.0881.112100
2.48-3.127.60.05656730.9970.0220.060.883100
3.12-507.90.04858890.9970.0180.0520.81499.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-3000data collection
HKL-3000data scaling
Cootmodel building
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD
Starting model: 4KAV

4kav


Resolution: 1.45→50 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.18 / WRfactor Rwork: 0.1513 / FOM work R set: 0.8856 / SU B: 2.065 / SU ML: 0.042 / SU R Cruickshank DPI: 0.0628 / SU Rfree: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1767 2715 5 %RANDOM
Rwork0.1515 ---
obs0.1527 52026 97.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 73.37 Å2 / Biso mean: 22.515 Å2 / Biso min: 11.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.1 Å2
Refinement stepCycle: final / Resolution: 1.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2530 0 15 492 3037
Biso mean--26.81 36.28 -
Num. residues----323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192653
X-RAY DIFFRACTIONr_bond_other_d0.0020.022446
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.9433615
X-RAY DIFFRACTIONr_angle_other_deg0.9633.0015650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.4465.102344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.04624.961127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12215436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0511511
X-RAY DIFFRACTIONr_chiral_restr0.0890.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023058
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02615
LS refinement shellResolution: 1.451→1.489 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 159 -
Rwork0.223 2837 -
all-2996 -
obs--72.88 %
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)
11.7694-0.9924-0.10186.0422-5.83376.51990.0543-0.18780.16970.4674-0.112-0.1015-0.43830.18530.05760.15090.00520.02420.139-0.0220.087828.41312.06424.185
21.4121-0.2523-0.54390.98610.11891.4033-0.0328-0.1420.0550.05290.0192-0.1054-0.04870.09230.01370.0349-0.0178-0.01710.03040.0090.034344.4993.98811.048
32.4931-0.0717-0.52414.3468-0.18544.5978-0.09970.1279-0.0425-0.2079-0.0153-0.4155-0.15630.42820.11490.16470.040.02830.15180.00540.229758.567-7.692-5.496
41.40060.0697-0.51611.0632-0.4451.7412-0.05690.0414-0.1212-0.06320.0147-0.01670.11870.00170.04230.0235-0.0078-0.0070.0054-0.00110.040543.29-1.9733.139
52.1363-0.2762-0.69870.72040.56363.0476-0.0981-0.0694-0.20910.10040.08640.16050.1475-0.30380.01180.0528-0.00390.01320.07820.03830.068828.2292.61912.352
67.1084-3.61571.09157.5521-0.37592.8767-0.0643-0.11210.2063-0.0808-0.05680.6133-0.2907-0.31530.12110.10230.0052-0.00850.1401-0.01820.120624.1395.4149.845
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A219 - 236
2X-RAY DIFFRACTION2A237 - 404
3X-RAY DIFFRACTION3A405 - 423
4X-RAY DIFFRACTION4A424 - 499
5X-RAY DIFFRACTION5A500 - 532
6X-RAY DIFFRACTION6A533 - 541

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