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- PDB-4lsf: Ion selectivity of OmpF soaked in 0.1M KBr -

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Basic information

Entry
Database: PDB / ID: 4lsf
TitleIon selectivity of OmpF soaked in 0.1M KBr
ComponentsOuter membrane protein F
KeywordsTRANSPORT PROTEIN / porin / outer membrane protein / beta-barrel / ion transport
Function / homology
Function and homology information


colicin transmembrane transporter activity / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion transmembrane transport / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / monoatomic ion channel activity ...colicin transmembrane transporter activity / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion transmembrane transport / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / monoatomic ion channel activity / lipid binding / membrane / identical protein binding
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
BROMIDE ION / Outer membrane porin F
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBalasundaresan, D. / Blachowicz, L. / Roux, B.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: A structural study of ion permeation in OmpF porin from anomalous X-ray diffraction and molecular dynamics simulations.
Authors: Dhakshnamoorthy, B. / Ziervogel, B.K. / Blachowicz, L. / Roux, B.
History
DepositionJul 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _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 F
B: Outer membrane protein F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,08611
Polymers74,3432
Non-polymers7449
Water3,621201
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)112,50915
Polymers111,5143
Non-polymers99512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_875-y+3,x-y+2,z1
crystal symmetry operation3_685-x+y+1,-x+3,z1
Buried area10840 Å2
ΔGint-58 kcal/mol
Surface area40340 Å2
MethodPISA
2
B: Outer membrane protein F
hetero molecules

B: Outer membrane protein F
hetero molecules

B: Outer membrane protein F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,74918
Polymers111,5143
Non-polymers1,23515
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-y+2,x-y+2,z1
crystal symmetry operation3_575-x+y,-x+2,z1
Buried area11060 Å2
ΔGint-55 kcal/mol
Surface area40670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.632, 116.632, 51.253
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-513-

HOH

21A-574-

HOH

31A-600-

HOH

41B-513-

HOH

51B-517-

HOH

61B-575-

HOH

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Components

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


Mass: 37171.301 Da / Num. of mol.: 2 / Fragment: UNP residues 23-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0929, cmlB, coa, cry, JW0912, ompF, tolF / Plasmid: PPR272 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: P02931
#2: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O

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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: 2.71 Å3/Da / Density % sol: 54.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50% PEG200, 0.1 M sodium cacodylate, 0.2 M magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.91956 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91956 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 61382 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 20
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.2_869) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OMF

2omf


Resolution: 1.9→29.158 Å / SU ML: 0.66 / σ(F): 1.96 / Phase error: 31.88 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2985 6099 5 %
Rwork0.2672 --
obs0.2687 61336 99.28 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.774 Å2 / ksol: 0.362 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.0565 Å2-0 Å20 Å2
2---8.0565 Å2-0 Å2
3---16.1129 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5238 0 19 201 5458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155406
X-RAY DIFFRACTIONf_angle_d1.5037320
X-RAY DIFFRACTIONf_dihedral_angle_d15.7441900
X-RAY DIFFRACTIONf_chiral_restr0.093741
X-RAY DIFFRACTIONf_plane_restr0.007990
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.38242000.37043671X-RAY DIFFRACTION96
1.9216-1.94420.35372010.3473909X-RAY DIFFRACTION99
1.9442-1.96790.36332100.353867X-RAY DIFFRACTION98
1.9679-1.99290.36372060.32623792X-RAY DIFFRACTION99
1.9929-2.01910.33442080.3143855X-RAY DIFFRACTION100
2.0191-2.04670.30952000.32163923X-RAY DIFFRACTION99
2.0467-2.0760.34592160.30853765X-RAY DIFFRACTION99
2.076-2.10690.29811920.2853833X-RAY DIFFRACTION100
2.1069-2.13980.30371890.28783916X-RAY DIFFRACTION99
2.1398-2.17490.30792140.30113834X-RAY DIFFRACTION100
2.1749-2.21240.32521940.28683905X-RAY DIFFRACTION100
2.2124-2.25260.29652120.27143910X-RAY DIFFRACTION99
2.2526-2.29590.34011990.28993826X-RAY DIFFRACTION100
2.2959-2.34280.33591980.29553937X-RAY DIFFRACTION99
2.3428-2.39370.2961970.27733863X-RAY DIFFRACTION99
2.3937-2.44940.28152080.27143872X-RAY DIFFRACTION99
2.4494-2.51060.34471770.27313841X-RAY DIFFRACTION100
2.5106-2.57840.29982110.2553881X-RAY DIFFRACTION99
2.5784-2.65420.3112000.24713902X-RAY DIFFRACTION99
2.6542-2.73980.26882150.25243826X-RAY DIFFRACTION100
2.7398-2.83770.3412030.26513933X-RAY DIFFRACTION100
2.8377-2.95120.3491880.27063855X-RAY DIFFRACTION100
2.9512-3.08540.31022110.27053808X-RAY DIFFRACTION99
3.0854-3.24780.3082180.25383910X-RAY DIFFRACTION99
3.2478-3.4510.28562070.24493887X-RAY DIFFRACTION99
3.451-3.7170.32651920.24213832X-RAY DIFFRACTION99
3.717-4.09010.2752000.24733888X-RAY DIFFRACTION100
4.0901-4.67990.24592040.22743910X-RAY DIFFRACTION100
4.6799-5.88820.2292200.24043855X-RAY DIFFRACTION100
5.8882-29.16140.3072090.33868X-RAY DIFFRACTION99

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