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- PDB-2xe2: Molecular insights into clinically isolated OmpC20 mutants and th... -

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Basic information

Entry
Database: PDB / ID: 2xe2
TitleMolecular insights into clinically isolated OmpC20 mutants and their role in multi-drug resistance
ComponentsOUTER MEMBRANE PORIN C
KeywordsTRANSPORT PROTEIN / CELL MEMBRANE / ION TRANSPORT
Function / homology
Function and homology information


porin activity / pore complex / cell outer membrane / monoatomic ion transmembrane transport
Similarity search - Function
Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / Porin / : / Porin domain superfamily / Porin ...Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / Porin / : / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
N-OCTYL-2-HYDROXYETHYL SULFOXIDE / Porin
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: 2IXW
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 PORIN C
B: OUTER MEMBRANE PORIN C
C: OUTER MEMBRANE PORIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,4666
Polymers114,8473
Non-polymers6193
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10430 Å2
ΔGint-54.2 kcal/mol
Surface area40970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.023, 74.198, 133.499
Angle α, β, γ (deg.)90.00, 124.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 38282.203 Da / Num. of mol.: 3
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: Q9K597
#2: Chemical ChemComp-OES / N-OCTYL-2-HYDROXYETHYL SULFOXIDE


Mass: 206.345 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS IS FROM A CLINICAL ISOLATE

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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: 2.27 Å3/Da / Density % sol: 45.77 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.5→110 Å / Num. obs: 33821 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 13
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.7 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0060refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XE1

2xe1


Resolution: 2.5→109.76 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.886 / SU B: 24.367 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R: 3.108 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25651 1788 5 %RANDOM
Rwork0.21676 ---
obs0.21873 33821 99.39 %-
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: 60.133 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0 Å20.23 Å2
2---0.09 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.5→109.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8127 0 39 222 8388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0218346
X-RAY DIFFRACTIONr_bond_other_d0.0020.025469
X-RAY DIFFRACTIONr_angle_refined_deg0.9911.92611286
X-RAY DIFFRACTIONr_angle_other_deg0.838313185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03651026
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61125480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.317151257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3981539
X-RAY DIFFRACTIONr_chiral_restr0.070.21128
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029771
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021881
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
Rfree0.339 105 -
Rwork0.297 2437 -
obs--94.92 %
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)
11.7633-0.749-0.42532.61310.65920.2075-0.02710.1493-0.101-0.2153-0.03120.13-0.0132-0.04750.05830.2491-0.03130.00780.23650.02290.350429.751-31.396-34.237
21.9981-0.0657-0.18881.70130.06340.8882-0.049-0.0317-0.20960.0136-0.00480.19180.1982-0.01710.05380.1787-0.02980.06170.16710.01360.428718.993-43.455-25.195
30.4125-0.581-0.03086.9861-9.051421.6877-0.1622-0.0211-0.09360.0623-0.15180.39240.21630.21580.31390.1032-0.00970.05940.2665-0.06470.65927.295-35.712-18.493
40.67290.7839-0.31061.9332-2.08033.1707-0.0926-0.02890.119-0.0530.06630.19320.0865-0.19770.02630.21380.03620.07370.2027-0.00020.559711.269-25.385-23.555
53.19060.33110.6431.91540.37660.21590.0120.20590.0565-0.2086-0.02630.02410.03750.08450.01430.25510.03050.11350.20350.02890.377236.891-14.117-34.291
61.88340.29470.0211.706-0.08621.63520.0152-0.01890.2539-0.0376-0.0406-0.0118-0.1015-0.08840.02540.21060.030.04510.1152-0.02420.39231.9961.297-25.252
76.4239-4.6004-5.51253.38474.73115.44810.4868-0.0831.4975-0.27930.0104-1.0319-0.6955-0.9205-0.49710.36-0.0840.06190.246-0.0550.883644.87.553-18.818
81.3675-0.7327-1.36571.21971.07263.80610.1342-0.16410.2763-0.0959-0.0056-0.2379-0.29950.1585-0.12850.2161-0.00220.04750.13950.03040.466351.49-1.144-23.897
92.519-0.0276-0.16722.2337-0.17950.0317-0.00620.1059-0.1788-0.1429-0.0525-0.12210.00510.01480.05870.20840.01090.05980.2641-0.01520.378848.255-28.967-34.453
102.1131-0.4844-0.43282.2118-0.21790.8152-0.044-0.2422-0.22750.1466-0.0477-0.45780.00020.21020.09170.12640.04440.0360.28930.09670.59264.236-32.431-25.769
118.6614.493710.89886.87325.787225.28580.3139-0.3962-1.45190.76380.056-1.0345-0.63710.509-0.370.2956-0.00880.020.20470.23751.074463.63-46.63-19.345
125.40590.49472.73041.1503-0.48694.2933-0.0419-0.3738-0.78890.2196-0.161-0.41210.16750.20060.20290.24310.07680.09340.19580.11660.700552.418-48.161-24.092
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 90
2X-RAY DIFFRACTION2A91 - 266
3X-RAY DIFFRACTION3A267 - 287
4X-RAY DIFFRACTION4A288 - 343
5X-RAY DIFFRACTION5B1 - 90
6X-RAY DIFFRACTION6B91 - 266
7X-RAY DIFFRACTION7B267 - 287
8X-RAY DIFFRACTION8B288 - 343
9X-RAY DIFFRACTION9C1 - 90
10X-RAY DIFFRACTION10C91 - 266
11X-RAY DIFFRACTION11C267 - 287
12X-RAY DIFFRACTION12C288 - 343

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