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- PDB-2xe1: Molecular insights into clinically isolated OmpC mutants and thei... -

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Basic information

Entry
Database: PDB / ID: 2xe1
TitleMolecular insights into clinically isolated OmpC mutants and their role in multi-drug resistance
ComponentsOUTER MEMBRANE PROTEIN C
KeywordsTRANSPORT PROTEIN / ION TRANSPORT / PORIN / ANTIBIOTIC RESISTANCE / CELL OUTER MEMBRANE / BETA BARREL / MEMBRANE PROTEIN
Function / homology
Function and homology information


porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane
Similarity search - Function
Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin, Gram-negative type / Porin / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DECANE / HEXANE / Outer membrane porin C
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBamford, V.A. / Naismith, J.H.
CitationJournal: Plos One / Year: 2011
Title: Altered Antibiotic Transport in Ompc Mutants Isolated from a Series of Clinical Strains of Multi-Drug Resistant E. Coli.
Authors: Lou, H. / Chen, M. / Black, S.S. / Bushell, S.R. / Ceccarelli, M. / Mach, T. / Beis, K. / Low, A.S. / Bamford, V.A. / Booth, I.R. / Bayley, H. / Naismith, J.H.
History
DepositionMay 10, 2010Deposition site: PDBE / Processing site: PDBE
SupersessionMay 19, 2010ID: 2IXX
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OUTER MEMBRANE PROTEIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5654
Polymers39,1941
Non-polymers3713
Water2,576143
1
A: OUTER MEMBRANE PROTEIN C
hetero molecules

A: OUTER MEMBRANE PROTEIN C
hetero molecules

A: OUTER MEMBRANE PROTEIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,69512
Polymers117,5833
Non-polymers1,1129
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area12100 Å2
ΔGint-21.7 kcal/mol
Surface area42310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.400, 120.400, 158.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein OUTER MEMBRANE PROTEIN C / PORIN OMPC / OUTER MEMBRANE PROTEIN 1B


Mass: 39194.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: O6 / Description: O6 UROPATHOGENIC STRAIN / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8CVW1
#2: Chemical ChemComp-D10 / DECANE / Decane


Mass: 142.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22
#3: Chemical ChemComp-HEX / HEXANE / Hexane


Mass: 86.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsHEXANE (HEX): MODEL FOR DETERGENT DECANE (D10): MODEL FOR DETERGENT

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.22 Å3/Da / Density % sol: 70.85 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→47 Å / Num. obs: 22833 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14
Reflection shellResolution: 2.5→2.5 Å / Redundancy: 9 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.4 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0060refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OSM

1osm


Resolution: 2.5→47.03 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.898 / SU B: 10.471 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21812 1213 5 %RANDOM
Rwork0.19287 ---
obs0.19414 22833 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.809 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å2-0 Å2
2--0.14 Å2-0 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2775 0 26 143 2944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0222865
X-RAY DIFFRACTIONr_bond_other_d0.0010.021876
X-RAY DIFFRACTIONr_angle_refined_deg0.8811.9253875
X-RAY DIFFRACTIONr_angle_other_deg0.69934533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3685355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04125.062162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.99615422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3711513
X-RAY DIFFRACTIONr_chiral_restr0.060.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023350
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02638
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 90 -
Rwork0.222 1652 -
obs--99.77 %
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)
11.95591.3518-1.41752.6603-1.36681.5250.1361-0.3144-0.01730.3623-0.16050.0425-0.09420.16040.02440.12420.001-0.03720.1186-0.00340.0429-50.70230.4690.237
20.95260.0805-0.17710.95170.54430.38180.0021-0.1394-0.12870.0563-0.0146-0.0830.04750.05290.01250.06910.0162-0.00490.0990.05920.07-46.77122.163-6.588
37.8717-3.951710.50944.1667-7.746319.82540.1485-0.2233-0.3550.06050.16090.12320.0272-0.3023-0.30950.0605-0.00970.04090.00970.00190.0751-48.73911.648-8.615
41.85780.29040.61251.3568-0.09011.79770.07320.0738-0.113-0.0061-0.0008-0.15580.24480.0587-0.07240.04390.02380.00520.04610.01330.0482-44.97313.965-17.424
50.78380.28910.20961.70340.77861.3656-0.02020.0135-0.0871-0.0496-0.0242-0.2028-0.02350.20880.04440.0252-0.0042-0.02390.10920.0530.0916-31.77927.679-12.122
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 58
2X-RAY DIFFRACTION2A59 - 133
3X-RAY DIFFRACTION3A134 - 163
4X-RAY DIFFRACTION4A164 - 220
5X-RAY DIFFRACTION5A221 - 354

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