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- PDB-3fyx: The Structure of OmpF porin with a synthetic dibenzo-18-crown-6 a... -

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Basic information

Entry
Database: PDB / ID: 3fyx
TitleThe Structure of OmpF porin with a synthetic dibenzo-18-crown-6 as modulator
ComponentsOuter membrane protein F
KeywordsTRANSPORT PROTEIN / beta-barrel / ion-channel engineering / porin structure / synthetic ion-current modulator / crown ether / Cell membrane / Cell outer membrane / Ion transport / Membrane / Phage recognition / Porin / Transmembrane / Transport
Function / homology
Function and homology information


colicin transmembrane transporter activity / porin activity / monoatomic ion channel complex / pore complex / protein homotrimerization / monoatomic ion channel activity / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / protein transport ...colicin transmembrane transporter activity / porin activity / monoatomic ion channel complex / pore complex / protein homotrimerization / monoatomic ion channel activity / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / protein transport / monoatomic ion transmembrane transport / lipid binding / identical protein binding / 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 ...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
Chem-451 / Outer membrane porin F
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsReitz, S. / Cebi, M. / Koert, U. / Essen, L.O.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2009
Title: On the function and structure of synthetically modified porins.
Authors: Reitz, S. / Cebi, M. / Reiss, P. / Studnik, G. / Linne, U. / Koert, U. / Essen, L.O.
History
DepositionJan 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane protein F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7443
Polymers37,0881
Non-polymers6562
Water00
1
A: Outer membrane protein F
hetero molecules

A: Outer membrane protein F
hetero molecules

A: Outer membrane protein F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,2329
Polymers111,2653
Non-polymers1,9676
Water0
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 area10220 Å2
ΔGint-40 kcal/mol
Surface area40060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.520, 135.520, 47.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Outer membrane protein F / Porin ompF / Outer membrane protein 1A / Outer membrane protein IA / Outer membrane protein B


Mass: 37088.215 Da / Num. of mol.: 1 / Mutation: K16C
Source method: isolated from a genetically manipulated source
Details: mutation K16C introduced by site-directed mutagenesis
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Strain: DH5-alpha / Gene: b0929, cmlB, coa, cry, JW0912, ompF, tolF / Plasmid: pET-20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) omp8 / References: UniProt: P02931
#2: Chemical ChemComp-451 / N-(6,7,9,10,17,18,20,21-octahydrodibenzo[b,k][1,4,7,10,13,16]hexaoxacyclooctadecin-2-yl)acetamide / N-(Dibenzo-18-crown-6-ether)-acetamide


Mass: 417.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27NO7
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM

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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: 3.4 Å3/Da / Density % sol: 63.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 0.2 M CaCl2, 48% PEG 400, 0.1 M Na-HEPES, pH 7.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.4→44.36 Å / Num. all: 7096 / Num. obs: 6991 / % possible obs: 98.8 % / Observed criterion σ(I): 0.6 / Redundancy: 5.4 % / Rmerge(I) obs: 0.17 / Rsym value: 0.17 / Net I/σ(I): 9.5
Reflection shellResolution: 3.4→3.6 Å / Redundancy: 4 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 5 / Rsym value: 0.274 / % possible all: 97.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OMF with K16 mutated to alanine

2omf


Resolution: 3.4→44.36 Å / Cor.coef. Fo:Fc: 0.83 / Cor.coef. Fo:Fc free: 0.765 / SU B: 37.337 / SU ML: 0.579 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.652 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29437 388 5.6 %RANDOM
Rwork0.2491 ---
obs0.25152 6601 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.37 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20.77 Å20 Å2
2--1.55 Å20 Å2
3----2.32 Å2
Refinement stepCycle: LAST / Resolution: 3.4→44.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2624 0 45 0 2669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222728
X-RAY DIFFRACTIONr_bond_other_d0.0030.0218
X-RAY DIFFRACTIONr_angle_refined_deg1.31.9483687
X-RAY DIFFRACTIONr_angle_other_deg3.005344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5525339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.84225146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.69415397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5341511
X-RAY DIFFRACTIONr_chiral_restr0.0880.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022180
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.21175
X-RAY DIFFRACTIONr_nbd_other0.1560.218
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21798
X-RAY DIFFRACTIONr_nbtor_other0.1030.29
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2117
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.2120
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4121.51685
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.74522614
X-RAY DIFFRACTIONr_scbond_it0.73231204
X-RAY DIFFRACTIONr_scangle_it1.0414.51073
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 30 -
Rwork0.324 459 -
obs--97.8 %

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