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- PDB-4jfb: Crystal structure of OmpF in C2 with tNCS -

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Basic information

Entry
Database: PDB / ID: 4jfb
TitleCrystal structure of OmpF in C2 with tNCS
ComponentsOuter membrane protein F
KeywordsMEMBRANE PROTEIN / porin / OmpF / E. coli outer membrane
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
Outer membrane porin F
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.801 Å
AuthorsWiseman, B. / Kilburg, A. / Chaptal, V. / Reyes-Meija, G.C. / Sarwan, J. / Falson, P. / Jault, J.M.
CitationJournal: PLoS ONE / Year: 2014
Title: Stubborn contaminants: influence of detergents on the purity of the multidrug ABC transporter BmrA
Authors: Wiseman, B. / Kilburg, A. / Chaptal, V. / Reyes-Mejia, G.C. / Sarwan, J. / Falson, P. / Jault, J.M.
History
DepositionFeb 28, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 8, 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


Theoretical massNumber of molelcules
Total (without water)222,6866
Polymers222,6866
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 area8850 Å2
ΔGint-53 kcal/mol
Surface area40740 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 area8810 Å2
ΔGint-52 kcal/mol
Surface area40490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.910, 110.880, 226.140
Angle α, β, γ (deg.)90.00, 104.46, 90.00
Int Tables number5
Space group name H-MC121

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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: 37114.250 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(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: 4.41 Å3/Da / Density % sol: 72.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 18-22% PEG 1500, 5-10% 2-Methyl-2,4-pentanediol, 0.1M Tris-HCl pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-110.97
SYNCHROTRONSOLEIL PROXIMA 120.97
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJul 15, 2012
PSI PILATUS 6M2PIXELFeb 23, 2013
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.971
21
ReflectionResolution: 3.8→68.57 Å / Num. all: 38450 / Num. obs: 32150 / % possible obs: 83.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.8→3.94 Å / % possible all: 28.55

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZFG

2zfg


Resolution: 3.801→68.57 Å / Occupancy max: 1 / Occupancy min: 0.02 / SU ML: 0.59 / σ(F): 1.95 / Phase error: 34.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3143 1581 4.94 %RANDOM
Rwork0.2616 ---
all0.2644 38450 --
obs0.2644 32028 83.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 304.67 Å2 / Biso mean: 113.0781 Å2 / Biso min: 14.36 Å2
Refinement stepCycle: LAST / Resolution: 3.801→68.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15762 0 0 0 15762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00616101
X-RAY DIFFRACTIONf_angle_d1.09721785
X-RAY DIFFRACTIONf_dihedral_angle_d13.0415629
X-RAY DIFFRACTIONf_chiral_restr0.0682210
X-RAY DIFFRACTIONf_plane_restr0.0042940
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.8006-3.92320.3372390.260790827
3.9232-4.06340.2817820.2655176553
4.0634-4.22610.29811190.2629237672
4.2261-4.41840.291340.2512300890
4.4184-4.65130.29721680.2433319997
4.6513-4.94260.33311700.2288319697
4.9426-5.32410.29441690.2248317497
5.3241-5.85970.3081820.2235321196
5.8597-6.7070.28161730.2356321897
6.707-8.44760.30841750.278322796
8.4476-68.58150.38841700.3282316593
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.19620.0065-0.9651.09190.02312.16980.2889-0.880.25520.10870.13450.0167-2.02591.59910.00061.0743-0.30290.01480.3259-0.24990.371585.0291-27.59933.627
20.8327-0.3874-0.21440.0838-0.12972.17510.30290.74290.2988-0.40410.22350.067-0.9827-2.66380.52160.56490.7633-0.02241.24360.22090.530850.6447-30.28116.8382
30.6168-0.2594-0.7131.01990.18122.9657-0.27450.1256-0.3821-0.08950.03530.02422.1443-0.89290.0730.8834-0.03410.19180.49640.18380.474469.8245-61.872626.2479
40.67250.3208-0.38670.5266-0.23620.67270.6977-0.45381.05010.38190.3605-0.1164-2.14111.74511.12731.4494-1.4790.10671.9902-0.81120.725658.0768-21.7537142.9114
51.56090.0012-0.58540.6841-0.40181.39640.6690.43740.7942-0.2541-0.2970.9239-2.1331-1.4175-0.13911.1621.14890.36382.82930.03081.123423.2672-24.2865126.9976
61.2227-0.6266-0.85991.6612-0.34612.6893-0.633-0.5638-0.72920.2537-0.40790.59062.15430.33490.06451.0723-0.16180.35911.47340.02380.573842.6194-56.0376135.9742
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:340)A1 - 340
2X-RAY DIFFRACTION2(chain B and resid 1:340)B1 - 340
3X-RAY DIFFRACTION3(chain C and resid 1:340)C1 - 340
4X-RAY DIFFRACTION4(chain D and resid 1:340)D1 - 340
5X-RAY DIFFRACTION5(chain E and resid 1:340)E1 - 340
6X-RAY DIFFRACTION6(chain F and resid 1:340)F1 - 340

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