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- PDB-3k19: OmpF porin -

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Basic information

Entry
Database: PDB / ID: 3k19
TitleOmpF porin
ComponentsOuter membrane protein F
KeywordsMEMBRANE PROTEIN / BETA BARREL / 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 / porin activity / pore complex / protein homotrimerization / monoatomic ion channel activity / monoatomic ion channel complex / cell outer membrane / lipopolysaccharide binding / disordered domain specific binding / protein transport ...colicin transmembrane transporter activity / porin activity / pore complex / protein homotrimerization / monoatomic ion channel activity / monoatomic ion channel complex / cell outer membrane / lipopolysaccharide binding / 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. / Gram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / Porin / : / Porin domain superfamily / Porin ...Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / Porin / : / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Outer membrane porin F
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.79 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
E: Outer membrane protein F
F: Outer membrane protein F
G: Outer membrane protein F
H: Outer membrane protein F
I: Outer membrane protein F
J: Outer membrane protein F
K: Outer membrane protein F
L: Outer membrane protein F


Theoretical massNumber of molelcules
Total (without water)445,37112
Polymers445,37112
Non-polymers00
Water00
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 area8730 Å2
ΔGint-52 kcal/mol
Surface area40350 Å2
MethodPISA
2
D: Outer membrane protein F
E: Outer membrane protein F
F: 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 area8700 Å2
ΔGint-52 kcal/mol
Surface area40370 Å2
MethodPISA
3
G: Outer membrane protein F
H: Outer membrane protein F
I: 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 area8740 Å2
ΔGint-52 kcal/mol
Surface area40350 Å2
MethodPISA
4
J: Outer membrane protein F
K: Outer membrane protein F
L: 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 area8670 Å2
ΔGint-52 kcal/mol
Surface area40390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.708, 210.522, 137.042
Angle α, β, γ (deg.)90.00, 100.49, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L

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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.: 12 / 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: 4.35 Å3/Da / Density % sol: 71.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 0.4 M NaH2PO4/1.6 M K2HPO4, 0.2M sodium chloride, 0.1M Imidazole pH 8, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2008
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.8→100 Å / Num. obs: 74966 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.137 / Rsym value: 0.137 / Net I/σ(I): 9.233
Reflection shellResolution: 3.8→3.87 Å / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.667 / Rsym value: 0.488 / % possible all: 100

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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: 3.79→49.57 Å / Cor.coef. Fo:Fc: 0.791 / Cor.coef. Fo:Fc free: 0.749 / SU B: 35.787 / SU ML: 0.499 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.741 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28794 3787 5.1 %RANDOM
Rwork0.28017 ---
obs0.28056 71179 49.57 %-
all-71179 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.133 Å2
Baniso -1Baniso -2Baniso -3
1-3.55 Å20 Å23.39 Å2
2---3.05 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 3.79→49.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31524 0 0 0 31524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.02232160
X-RAY DIFFRACTIONr_angle_refined_deg0.651.93143504
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1954060
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.00724.9891748
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.579154796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.73715132
X-RAY DIFFRACTIONr_chiral_restr0.0440.24412
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0225848
X-RAY DIFFRACTIONr_mcbond_it0.091.519848
X-RAY DIFFRACTIONr_mcangle_it0.185231324
X-RAY DIFFRACTIONr_scbond_it0.272312312
X-RAY DIFFRACTIONr_scangle_it0.4774.512180
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2619 / Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0.01 Å

Auth asym-IDTypeWeight position
Atight positional0.05
Btight positional0.05
Ctight positional0.05
Dtight positional0.05
Etight positional0.05
Ftight positional0.05
Gtight positional0.05
Htight positional0.05
Itight positional0.05
Jtight positional0.05
Ktight positional0.05
Ltight positional0.05
Atight thermal0.5
Btight thermal0.5
Ctight thermal0.5
Dtight thermal0.5
Etight thermal0.5
Ftight thermal0.5
Gtight thermal0.5
Htight thermal0.5
Itight thermal0.5
Jtight thermal0.5
Ktight thermal0.5
Ltight thermal0.5
LS refinement shellResolution: 3.787→3.885 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 272 -
Rwork0.344 4598 -
obs--87.46 %

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