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Basic information

Entry
Database: PDB / ID: 2xe3
TitleOmpC28
ComponentsOUTER MEMBRANE PORIN C
KeywordsTRANSPORT PROTEIN / CELL MEMBRANE / ION TRANSPORT / PORIN
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. / Porin domain, Gram-negative type / Gram-negative porin / Porin, Gram-negative type / Porin / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsLou, H. / 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
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 16, 2011Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OUTER MEMBRANE PORIN C
B: OUTER MEMBRANE PORIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2974
Polymers76,7132
Non-polymers5852
Water54030
1
A: OUTER MEMBRANE PORIN C
hetero molecules

A: OUTER MEMBRANE PORIN C
hetero molecules

A: OUTER MEMBRANE PORIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,9466
Polymers115,0693
Non-polymers8773
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area11650 Å2
ΔGint-45.8 kcal/mol
Surface area40350 Å2
MethodPISA
2
B: OUTER MEMBRANE PORIN C
hetero molecules

B: OUTER MEMBRANE PORIN C
hetero molecules

B: OUTER MEMBRANE PORIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,9466
Polymers115,0693
Non-polymers8773
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area11540 Å2
ΔGint-42.4 kcal/mol
Surface area40460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.489, 103.489, 186.492
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-2003-

HOH

21B-2001-

HOH

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Components

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


Mass: 38356.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: O6 / Description: CLINICAL ISOLATE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9K597
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS IS FROM A CLINICAL SEQUENCE DESCRIBED IN PUBMED ID: 11722730. A.S.LOW,F.M.MACKENZIE,I.M.GOULD, ...THIS IS FROM A CLINICAL SEQUENCE DESCRIBED IN PUBMED ID: 11722730. A.S.LOW,F.M.MACKENZIE,I.M.GOULD, I.R.BOOTH. PROTECTED ENVIRONMENTS ALLOW PARALLEL EVOLUTION OF A BACTERIAL PATHOGEN IN A PATIENT SUBJECTED TO LONG-TERM ANTIBIOTIC THERAPY. MOL.MICROBIOL. 42,619

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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: 3.77 Å3/Da / Density % sol: 67.37 % / 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: 2.85→2.9 Å / Num. obs: 24149 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 15.5
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 8 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.8 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.6.0073refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XE1

2xe1


Resolution: 2.85→49.88 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.918 / SU B: 28.482 / SU ML: 0.254 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.005 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1301 5.1 %RANDOM
Rwork0.214 ---
obs0.215 24149 96.4 %-
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: 28.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.81 Å20.91 Å2-0 Å2
2--1.81 Å2-0 Å2
3----2.72 Å2
Refinement stepCycle: LAST / Resolution: 2.85→49.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5430 0 40 30 5500
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225594
X-RAY DIFFRACTIONr_bond_other_d0.0010.023622
X-RAY DIFFRACTIONr_angle_refined_deg0.9211.9317568
X-RAY DIFFRACTIONr_angle_other_deg0.72538728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6485684
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62124.969322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00315840
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.731526
X-RAY DIFFRACTIONr_chiral_restr0.0620.2760
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026528
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021264
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: 2.85→2.92 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.288 1790 -
Rfree-98 -
obs--97.42 %
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)
12.8357-0.24-0.37182.4507-0.31981.7081-0.0574-0.12840.37210.0673-0.1265-0.484-0.33140.35640.18390.0985-0.0878-0.05930.1060.02260.196-34.154-16.7291.339
22.4060.08350.44562.5420.3640.7531-0.1156-0.01040.4089-0.024-0.0505-0.3756-0.18990.15330.16610.0807-0.0326-0.03030.090.05050.1819-36.58-13.97156.932
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 343
2X-RAY DIFFRACTION2B1 - 343

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