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- PDB-6sut: Crystal structure of phosphothreonine MCR-2 -

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Basic information

Entry
Database: PDB / ID: 6sut
TitleCrystal structure of phosphothreonine MCR-2
ComponentsPutative integral membrane protein
KeywordsANTIMICROBIAL PROTEIN / colistin / MCR / phosphoethanolamine / transferase
Function / homology
Function and homology information


transferase activity, transferring phosphorus-containing groups / sulfuric ester hydrolase activity / 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
BROMIDE ION / Putative integral membrane protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsHinchliffe, P. / Spencer, J.
CitationJournal: Chem.Commun.(Camb.) / Year: 2020
Title: Resistance to the "last resort" antibiotic colistin: a single-zinc mechanism for phosphointermediate formation in MCR enzymes.
Authors: Lythell, E. / Suardiaz, R. / Hinchliffe, P. / Hanpaibool, C. / Visitsatthawong, S. / Oliveira, A.S.F. / Lang, E.J.M. / Surawatanawong, P. / Lee, V.S. / Rungrotmongkol, T. / Fey, N. / ...Authors: Lythell, E. / Suardiaz, R. / Hinchliffe, P. / Hanpaibool, C. / Visitsatthawong, S. / Oliveira, A.S.F. / Lang, E.J.M. / Surawatanawong, P. / Lee, V.S. / Rungrotmongkol, T. / Fey, N. / Spencer, J. / Mulholland, A.J.
History
DepositionSep 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative integral membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6757
Polymers36,1611
Non-polymers5146
Water7,999444
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-0 kcal/mol
Surface area13250 Å2
Unit cell
Length a, b, c (Å)43.080, 53.570, 122.669
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Putative integral membrane protein


Mass: 36161.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mcr-2 / Production host: Escherichia coli (E. coli) / Strain (production host): SoluBL21 / References: UniProt: A0A1C3NEV1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / 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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 444 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.96 Å3/Da / Density % sol: 37.15 %
Crystal growTemperature: 292 K / Method: vapor diffusion
Details: 0.15 M potassium bromide, 30% PEG2000MME Protein: 15 mg/ml in 10 mM NaPi pH7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.911 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.911 Å / Relative weight: 1
ReflectionResolution: 1.2→53.57 Å / Num. obs: 87793 / % possible obs: 98.1 % / Redundancy: 10 % / Biso Wilson estimate: 10.8490655323 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.034 / Net I/σ(I): 11.7
Reflection shellResolution: 1.2→1.22 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4367 / CC1/2: 0.623 / Rpim(I) all: 0.426 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MX9

5mx9


Resolution: 1.2→49.09 Å / SU ML: 0.0938913037912 / Cross valid method: FREE R-VALUE / σ(F): 1.33789850815 / Phase error: 14.6461024616
RfactorNum. reflection% reflection
Rfree0.153780431788 4277 4.87690851663 %
Rwork0.141051462457 --
obs0.141659840596 87699 97.8881807324 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 17.02196251 Å2
Refinement stepCycle: LAST / Resolution: 1.2→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2541 0 26 444 3011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007566451702872681
X-RAY DIFFRACTIONf_angle_d0.9600984408383656
X-RAY DIFFRACTIONf_chiral_restr0.0776142061777398
X-RAY DIFFRACTIONf_plane_restr0.00669745613111481
X-RAY DIFFRACTIONf_dihedral_angle_d16.9378721896977
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.21360.2562922717841410.2693188011262694X-RAY DIFFRACTION97.022587269
1.2136-1.22790.2546170975271330.2437810393062734X-RAY DIFFRACTION95.2808241941
1.2279-1.24290.2261430021531620.235718408582623X-RAY DIFFRACTION96.3667820069
1.2429-1.25860.2450303568151080.2281605252832725X-RAY DIFFRACTION96.7885206696
1.2586-1.27520.2204521959091380.2140241462092724X-RAY DIFFRACTION95.6231206148
1.2752-1.29270.210009943311430.2153609928792706X-RAY DIFFRACTION96.8718123087
1.2927-1.31110.2133036246181320.2102453994792716X-RAY DIFFRACTION96.64065151
1.3111-1.33070.2347956990721610.2011231067822672X-RAY DIFFRACTION96.8215994532
1.3307-1.35150.1951493099221360.203457898572764X-RAY DIFFRACTION97.1198928332
1.3515-1.37370.1801121424481460.1812011950272716X-RAY DIFFRACTION96.8200270636
1.3737-1.39730.1967264849011420.1900803933712738X-RAY DIFFRACTION97.4949221395
1.3973-1.42280.1922408236681400.1681638856382717X-RAY DIFFRACTION97.0118845501
1.4228-1.45010.1811097262411360.1587201789322782X-RAY DIFFRACTION98.0840336134
1.4501-1.47970.1759180578041410.154682572832712X-RAY DIFFRACTION96.6136132746
1.4797-1.51190.1819488375641640.1470553750982766X-RAY DIFFRACTION98.7196765499
1.5119-1.54710.1546389945951450.141575717772741X-RAY DIFFRACTION97.0084033613
1.5471-1.58580.1439550332411260.1403217419592791X-RAY DIFFRACTION98.2485685416
1.5858-1.62860.1422971753591830.1340487854022767X-RAY DIFFRACTION98.9600805099
1.6286-1.67660.1662512994191490.1371652038472775X-RAY DIFFRACTION97.6946207818
1.6766-1.73070.12939101171380.1323756944882777X-RAY DIFFRACTION97.9831932773
1.7307-1.79250.149092969141410.1301079677372790X-RAY DIFFRACTION98.6204576043
1.7925-1.86430.1374637838461260.1318896065132840X-RAY DIFFRACTION99.0317195326
1.8643-1.94920.1384072177311500.1234710398692800X-RAY DIFFRACTION98.9268947015
1.9492-2.05190.1264136623571260.1226980959072847X-RAY DIFFRACTION98.7379608104
2.0519-2.18050.1300071239781450.1206260426472831X-RAY DIFFRACTION99.4320080187
2.1805-2.34880.1206763220931530.1226351907622858X-RAY DIFFRACTION99.471423852
2.3488-2.58520.1190374700831470.1185979930972868X-RAY DIFFRACTION99.4721214121
2.5852-2.95930.1501701447671370.1254928139632905X-RAY DIFFRACTION99.7050147493
2.9593-3.72820.1441109620031420.1215052523982942X-RAY DIFFRACTION99.8381353189
3.7282-49.090.1502603975461460.1336653026223101X-RAY DIFFRACTION99.8769609351
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)
14.64705782349-5.576338134810.07059945884377.05134511503-0.2135077839582.15423479023-0.312981768175-0.2912565210560.1431253865670.6835477922450.242628466865-0.2502224428240.113995887190.05973223753990.07139475580480.207461724127-0.0354221361757-0.02902969535920.164665610614-0.01997907032350.10756058222515.43402697744.678592375163.79830162471
20.7536692868530.2232213579340.1907533030620.9386842757560.4072652960340.748036615271-6.85564418475E-5-0.0269940649901-0.09171484303440.081480392543-0.02230801716450.03146954001880.0868299368898-0.01872202062860.01588585282640.0807116246134-0.004583196785150.01567959453190.07047093330820.003756531357480.08006141099425.16805623194-6.55421617115-19.8250121658
34.82403454692-1.029904197180.5750823336643.208189937131.224170182894.46522449028-0.0796565685522-0.1399830089820.1330491943060.0275285131155-0.04520832764250.26054671809-0.248294617759-0.3070754042090.08825035820830.1068120754490.007936969880350.01190706112810.0938675315091-0.01635416915670.07806850970282.2207427311611.7207115133-8.19105669552
40.840566469237-0.0728184348892-0.1252936330570.8517313179850.2738355351381.1902692489-0.0137127075059-0.01599013297660.02316598649130.02856102907180.0205469475419-0.0942206802462-0.05157014305480.0675041119583-0.01441475872910.0782671904737-0.0196817242921-0.0009758107622030.0906776785099-0.01581027882910.094732246809619.48641899577.1611752549-18.2903250746
51.213515309670.3728706481472.26492238350.9248455864871.023698878816.50945251496-0.04324123988940.0516828825-0.01337609886360.02496781495950.0461641509024-0.0399656707616-0.06886417214130.142330312903-0.001322631834830.0456858991328-0.0162496228380.02379368423830.0549712378564-0.0009991821096670.072992129221314.59876637410.711134269106-24.2735108875
67.23313655093-6.186946286261.402485393067.77746296547-1.371828207223.083014411720.2417827766190.3719560181840.151280400118-0.418831923072-0.2352626470410.0340771040599-0.158491201651-0.0316819234745-0.02076114265360.13516588179-0.00739381491803-0.004523739811270.116960976242-0.01193151489860.08413079376822.07290323632-1.89050620519-41.3857050608
75.78176517644-0.6550366331625.94190435210.929552485818-0.3361082808037.00698409540.06295485174240.0763933594891-0.1204293152050.01202944274750.028304164935-0.03795539035340.07372971073550.114931954493-0.09312139636280.0552257975741-0.004549954907980.01153838804540.0471732600667-0.007829866399980.066539348207412.4194470462-7.07509869335-26.3575525279
81.03754337055-0.2815899515991.111348126110.846717073033-0.2797635712061.65012243760.04359828235690.05986257331370.01592993075760.0284855938733-0.06972860616020.01150967910430.06751794231510.05835665086070.04660248448680.0580085327837-0.01093306125970.01732058779410.0610065666224-0.005629146234240.05985171183172.45655599098-0.296326592515-20.6754945638
93.29575590671-1.843439936281.179218221832.42853616268-1.099371616911.55405905276-0.027300127915-0.176621293634-0.1966741706230.1816571114990.03821670708630.05702549661940.133985826071-0.0386269241875-0.03799781112310.13047271956-0.01586528720940.01843523331880.0730348954905-0.0002786244318360.1012507680354.90937857526-8.94298071797-11.9324102249
101.84330955681-0.05497300115541.026418847241.327989273720.5276354607522.11501455468-0.00261859489169-0.34268292537-0.07738825340130.4315499743140.01932684086180.09386632470360.122596656101-0.169029916463-0.01640933893550.194504536712-0.006518129302410.02810725302290.1421638378350.01144728866430.07741846953996.38953997453-1.52779032431-1.86578775677
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 217 through 237 )
2X-RAY DIFFRACTION2chain 'A' and (resid 238 through 287 )
3X-RAY DIFFRACTION3chain 'A' and (resid 288 through 311 )
4X-RAY DIFFRACTION4chain 'A' and (resid 312 through 379 )
5X-RAY DIFFRACTION5chain 'A' and (resid 380 through 407 )
6X-RAY DIFFRACTION6chain 'A' and (resid 408 through 423 )
7X-RAY DIFFRACTION7chain 'A' and (resid 424 through 452 )
8X-RAY DIFFRACTION8chain 'A' and (resid 453 through 486 )
9X-RAY DIFFRACTION9chain 'A' and (resid 487 through 513 )
10X-RAY DIFFRACTION10chain 'A' and (resid 514 through 540 )

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