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- PDB-4lsi: Ion selectivity of OmpF porin soaked in 0.3M KBr -

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Basic information

Entry
Database: PDB / ID: 4lsi
TitleIon selectivity of OmpF porin soaked in 0.3M 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 / protein transport ...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 / protein transport / monoatomic ion channel activity / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
BROMIDE ION / DI(HYDROXYETHYL)ETHER / Outer membrane porin F
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.089 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
C: Outer membrane protein F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,97737
Polymers111,5143
Non-polymers3,46334
Water10,323573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15230 Å2
ΔGint-57 kcal/mol
Surface area40440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.094, 116.559, 53.592
Angle α, β, γ (deg.)90.00, 97.00, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-688-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#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.: 3 / 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

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Non-polymers , 6 types, 607 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Br
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 573 / 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: 2.81 Å3/Da / Density % sol: 56.21 %
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, crystals soaked in 0.3 M potassium bromide, 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: 2.089→50 Å / Num. obs: 71693 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 13.6
Reflection shellResolution: 2.089→2.14 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 1.78 / % possible all: 99.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OMF

2omf


Resolution: 2.089→32.74 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.708 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.202 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24534 3611 5 %RANDOM
Rwork0.18974 ---
obs0.19252 68077 98.26 %-
all-71693 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.356 Å2
Baniso -1Baniso -2Baniso -3
1--2.18 Å2-0 Å2-0.24 Å2
2---1.22 Å2-0 Å2
3---3.33 Å2
Refinement stepCycle: LAST / Resolution: 2.089→32.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7728 0 153 573 8454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.028033
X-RAY DIFFRACTIONr_bond_other_d0.0010.027196
X-RAY DIFFRACTIONr_angle_refined_deg1.9931.9410813
X-RAY DIFFRACTIONr_angle_other_deg1.276316474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6675999
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.22324.931432
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.128151173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8621533
X-RAY DIFFRACTIONr_chiral_restr0.1350.21087
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029588
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022055
LS refinement shellResolution: 2.089→2.143 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 265 -
Rwork0.268 4815 -
obs--93.74 %

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