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- PDB-3k1b: Structure of OmpF porin -

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Basic information

Entry
Database: PDB / ID: 3k1b
TitleStructure of OmpF porin
ComponentsOuter membrane protein F
KeywordsMEMBRANE PROTEIN / OmpF porin / FOSCHOLINE-12 / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structures of Membrane Proteins / CSMP / Cell membrane / Cell outer membrane / Ion transport / Membrane / Phage recognition / Porin / Transmembrane / Transport / TRANSPORT PROTEIN
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 domain superfamily
Similarity search - Domain/homology
Outer membrane porin F
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.39 Å
AuthorsKefala, G. / Ahn, C. / Krupa, M. / Maslennikov, I. / Kwiatkowski, W. / Choe, S. / Center for Structures of Membrane Proteins (CSMP)
CitationJournal: Protein Sci. / Year: 2010
Title: Structures of the OmpF porin crystallized in the presence of foscholine-12.
Authors: Kefala, G. / Ahn, C. / Krupa, M. / Esquivies, L. / Maslennikov, I. / Kwiatkowski, W. / Choe, S.
History
DepositionSep 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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 protein F
B: Outer membrane protein F
C: Outer membrane protein F
D: Outer membrane protein F


Theoretical massNumber of molelcules
Total (without water)148,4574
Polymers148,4574
Non-polymers00
Water0
1
A: Outer membrane protein F
B: Outer membrane protein F
C: Outer membrane protein F


Theoretical massNumber of molelcules
Total (without water)111,3433
Polymers111,3433
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8840 Å2
ΔGint-55 kcal/mol
Surface area40820 Å2
MethodPISA
2
D: Outer membrane protein F

D: Outer membrane protein F

D: Outer membrane protein F


Theoretical massNumber of molelcules
Total (without water)111,3433
Polymers111,3433
Non-polymers00
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 area8880 Å2
ΔGint-50 kcal/mol
Surface area39540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)215.529, 215.529, 137.465
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: 37114.250 Da / Num. of mol.: 4 / Fragment: sequence database residues 1-340 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: Bl21(DE3) / References: UniProt: P02931

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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: 6.21 Å3/Da / Density % sol: 80.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 3.9
Details: 0.48 sodium phosphate monobasic, 0.72 M potassium phosphate monobasic, 0.1 M acetate pH 3.9, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2009
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 4.4→50 Å / Num. obs: 23572 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.211 / Rsym value: 0.211 / Net I/σ(I): 7.778
Reflection shellResolution: 4.4→4.48 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 3 / Num. unique all: 137454 / Rsym value: 0.512 / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
BALBESphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OMF

2omf


Resolution: 4.39→50 Å / Cor.coef. Fo:Fc: 0.796 / Cor.coef. Fo:Fc free: 0.761 / SU B: 53.658 / SU ML: 0.668 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.011 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32887 1211 5.1 %RANDOM
Rwork0.26366 ---
obs0.26695 22361 99 %-
all-22361 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 126.423 Å2
Baniso -1Baniso -2Baniso -3
1--5.41 Å2-2.71 Å20 Å2
2---5.41 Å20 Å2
3---8.12 Å2
Refinement stepCycle: LAST / Resolution: 4.39→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10508 0 0 0 10508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.02210723
X-RAY DIFFRACTIONr_angle_refined_deg2.8571.93114506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.78451354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.64424.991583
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.659151599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.8411544
X-RAY DIFFRACTIONr_chiral_restr0.170.21471
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028620
X-RAY DIFFRACTIONr_mcbond_it0.7531.56618
X-RAY DIFFRACTIONr_mcangle_it1.513210445
X-RAY DIFFRACTIONr_scbond_it1.9434105
X-RAY DIFFRACTIONr_scangle_it3.4654.54061
LS refinement shellResolution: 4.394→4.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 71 -
Rwork0.28 1621 -
obs--98.14 %

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