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- PDB-6bne: Crystal structure of the intrinsic colistin resistance enzyme ICR... -

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Basic information

Entry
Database: PDB / ID: 6bne
TitleCrystal structure of the intrinsic colistin resistance enzyme ICR(Mc) from Moraxella catarrhalis, catalytic domain, phosphate-bound complex
ComponentsPhosphoethanolamine transferase
KeywordsTRANSFERASE / antibiotic resistance / colistin / polymycin / phosphoethanolamine transferase / sulfatase fold / alpha/beta protein / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


phosphotransferase activity, phosphate group as acceptor / lipopolysaccharide core region biosynthetic process / metal ion binding / 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
ACETATE ION / PHOSPHATE ION / Phosphoethanolamine transferase
Similarity search - Component
Biological speciesMoraxella sp. HMSC061H09 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsStogios, P.J. / Evdokimova, E. / Wawrzak, Z. / Di Leo, R. / Savchenko, A. / Anderson, W.F. / Satchell, K.J. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Substrate recognition by a colistin resistance enzyme from Moraxella catarrhalis.
Authors: Stogios, P.J. / Cox, G. / Zubyk, H.L. / Evdokimova, E. / Wawrzak, Z. / Wright, G.D. / Savchenko, A.
History
DepositionNov 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoethanolamine transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5067
Polymers37,9711
Non-polymers5346
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)147.524, 147.524, 147.524
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphoethanolamine transferase


Mass: 37971.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moraxella sp. HMSC061H09 (bacteria) / Gene: HMPREF2573_04170 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: A0A1E9VP98

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Non-polymers , 5 types, 122 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.52 Å3/Da / Density % sol: 65.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate pH 4.6, 1.2 M ammonium sulfate, cryoprotectant 8% glycerol, 8% ethylene glycol and 8% sucrose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.27424 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27424 Å / Relative weight: 1
ReflectionResolution: 2.61→104.32 Å / Num. obs: 17315 / % possible obs: 100 % / Redundancy: 77.3 % / CC1/2: 1 / Rpim(I) all: 0.028 / Rsym value: 0.181 / Net I/σ(I): 24.7
Reflection shellResolution: 2.61→2.68 Å / Redundancy: 79.5 % / Rmerge(I) obs: 3.313 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1250 / CC1/2: 0.84 / Rpim(I) all: 0.515 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2733: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphenix.phaserphasing
PHENIXphenix.autobuildmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KAY

4kay


Resolution: 2.61→60.226 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2705 830 5.02 %RANDOM
Rwork0.234 ---
obs0.2358 16528 95.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.61→60.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2602 0 30 116 2748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062689
X-RAY DIFFRACTIONf_angle_d1.383666
X-RAY DIFFRACTIONf_dihedral_angle_d13.067958
X-RAY DIFFRACTIONf_chiral_restr0.07407
X-RAY DIFFRACTIONf_plane_restr0.006480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6103-2.77390.48721150.48012354X-RAY DIFFRACTION88
2.7739-2.9880.41411470.34092650X-RAY DIFFRACTION99
2.988-3.28870.30691380.27632675X-RAY DIFFRACTION100
3.2887-3.76450.33381220.27582474X-RAY DIFFRACTION91
3.7645-4.74260.23161620.18062625X-RAY DIFFRACTION96
4.7426-60.24240.21251460.19322920X-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)
13.57780.52770.43285.75940.74312.10310.07510.12510.04750.4903-0.1187-0.59260.18170.37660.03460.46390.1025-0.06060.6544-0.02840.5617-1.614533.2738-22.6078
23.23841.67771.4136.4350.026.5286-0.22160.10150.52730.64470.15270.2528-0.587-0.51450.07090.48380.1140.02780.529-0.07860.5283-6.889847.6967-23.808
36.31562.5691-0.74664.1871-0.99811.9026-0.00750.9884-0.0311-0.12060.11470.0592-0.02240.0417-0.08820.39570.0982-0.00220.6833-0.08380.4387-15.557435.5657-33.4867
49.15211.9128-1.4084.5438-2.11363.6202-0.0811-0.2705-0.66240.2739-0.1664-0.58740.18520.50990.25570.44360.0946-0.01630.552-0.06450.5644-2.455128.5242-22.8446
55.27621.7869-4.0188.9091.53014.07440.0249-0.26150.81930.05060.3733-2.4983-0.5291.8927-0.49270.72710.1166-0.1971.0217-0.15641.666511.932230.7377-22.3021
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 243:342)
2X-RAY DIFFRACTION2(chain A and resid 343:383)
3X-RAY DIFFRACTION3(chain A and resid 384:488)
4X-RAY DIFFRACTION4(chain A and resid 489:566)
5X-RAY DIFFRACTION5(chain A and resid 567:578)

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