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- PDB-8c7l: Serendipitous structure of OmpF contaminant in space group P21. -

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Basic information

Entry
Database: PDB / ID: 8c7l
TitleSerendipitous structure of OmpF contaminant in space group P21.
ComponentsOuter membrane porin F
KeywordsMEMBRANE PROTEIN / contaminant / pore
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 domain superfamily
Similarity search - Domain/homology
Outer membrane porin F
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.52 Å
AuthorsBloch, Y. / Theunissen, S. / Savvides, S.N.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)12S0519N Belgium
Citation
Journal: To Be Published
Title: Serendipitous structure of OmpF contaminant in space group P21.
Authors: Bloch, Y. / Theunissen, S. / Savvides, S.N.
#1: Journal: Biochem Biophys Res Commun / Year: 2009
Title: The agglutination protein AggA from Shewanella oneidensis MR-1 is a TolC-like protein and forms active channels in vitro.
Authors: Theunissen, S. / Vergauwen, B. / De Smet, L. / Van Beeumen, J. / Van Gelder, P. / Savvides, S.N.
History
DepositionJan 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane porin F
B: Outer membrane porin F
C: Outer membrane porin F
D: Outer membrane porin F
E: Outer membrane porin F
F: Outer membrane porin F


Theoretical massNumber of molelcules
Total (without water)236,1906
Polymers236,1906
Non-polymers00
Water00
1
A: Outer membrane porin F
B: Outer membrane porin F
C: Outer membrane porin F


Theoretical massNumber of molelcules
Total (without water)118,0953
Polymers118,0953
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Outer membrane porin F
E: Outer membrane porin F
F: Outer membrane porin F


Theoretical massNumber of molelcules
Total (without water)118,0953
Polymers118,0953
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.811, 151.002, 109.658
Angle α, β, γ (deg.)90.000, 117.936, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 11 or resid 13...
d_2ens_1(chain "B" and (resid 1 through 11 or resid 13...
d_3ens_1(chain "C" and (resid 1 through 11 or resid 13...
d_4ens_1(chain "D" and (resid 1 through 11 or resid 13...
d_5ens_1(chain "E" and (resid 1 through 11 or resid 13...
d_6ens_1(chain "F" and (resid 1 through 11 or resid 13...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAVALA1 - 11
d_12ens_1LEULEUA13 - 55
d_13ens_1GLYGLYA57 - 217
d_14ens_1LYSTHRA219 - 247
d_15ens_1GLYASPA249 - 256
d_16ens_1LEUGLUA258 - 296
d_17ens_1GLYSERA298 - 308
d_18ens_1TYRPHEA310 - 340
d_21ens_1ALAVALB1 - 11
d_22ens_1LEULEUB13 - 55
d_23ens_1GLYGLYB57 - 217
d_24ens_1LYSTHRB219 - 247
d_25ens_1GLYASPB249 - 256
d_26ens_1LEUGLUB258 - 296
d_27ens_1GLYSERB298 - 308
d_28ens_1TYRPHEB310 - 340
d_31ens_1ALAVALC1 - 11
d_32ens_1LEULEUC13 - 55
d_33ens_1GLYGLYC57 - 217
d_34ens_1LYSTHRC219 - 247
d_35ens_1GLYASPC249 - 256
d_36ens_1LEUGLUC258 - 296
d_37ens_1GLYSERC298 - 308
d_38ens_1TYRPHEC310 - 340
d_41ens_1ALAVALD1 - 11
d_42ens_1LEULEUD13 - 55
d_43ens_1GLYGLYD57 - 217
d_44ens_1LYSTHRD219 - 247
d_45ens_1GLYASPD249 - 256
d_46ens_1LEUGLUD258 - 296
d_47ens_1GLYSERD298 - 308
d_48ens_1TYRPHED310 - 340
d_51ens_1ALAVALE1 - 11
d_52ens_1LEULEUE13 - 55
d_53ens_1GLYGLYE57 - 217
d_54ens_1LYSTHRE219 - 247
d_55ens_1GLYASPE249 - 256
d_56ens_1LEUGLUE258 - 296
d_57ens_1GLYSERE298 - 308
d_58ens_1TYRPHEE310 - 340
d_61ens_1ALAVALF1 - 11
d_62ens_1LEULEUF13 - 55
d_63ens_1GLYGLYF57 - 217
d_64ens_1LYSTHRF219 - 247
d_65ens_1GLYASPF249 - 256
d_66ens_1LEUGLUF258 - 296
d_67ens_1GLYSERF298 - 308
d_68ens_1TYRPHEF310 - 340

NCS oper:
IDCodeMatrixVector
1given(0.958621660243, -0.281988104792, -0.0390796784501), (-0.104007640449, -0.474697063516, 0.873982327405), (-0.265003628731, -0.833753804576, -0.484383804555)-3.15626736526, -42.9676559225, 24.3282840515
2given(0.957733073111, -0.0922734271038, -0.27245729082), (-0.282828775395, -0.474890243274, -0.833358950664), (-0.0524904227337, 0.875194190734, -0.48091567247)5.37142585654, -1.03734363337, 49.5220831642
3given(-0.999983750699, -0.00350189103529, 0.00449834379955), (-0.00225345280747, -0.481996428094, -0.876170283253), (0.00523643850403, -0.876166182904, 0.481980704643)-25.6494653728, 0.0677472629474, -0.169322190705
4given(-0.957519159715, 0.0963257460956, 0.271805830362), (0.180020816668, -0.536665319795, 0.824368145973), (0.225276639592, 0.838279001985, 0.49652668658)-30.823840831, -42.7664681297, 24.6718826077
5given(-0.958813836033, 0.281687908072, 0.0364410520836), (0.281947517631, 0.959427560229, 0.00208661792698), (-0.0343747746539, 0.0122751423137, -0.999333625847)-22.3088604784, -0.520388698391, 49.2668654175

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Components

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


Mass: 39365.043 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Details: Residues [1-22] expected to be part of signal peptide.
Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Variant: STAR / 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: 3.25 Å3/Da / Density % sol: 62.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1mM NaCl, 0.1 MgCl2, 0.1 mM NaAcetate pH 4.5, 30% PEG400 copurified after refolding with 0.2 % lauryl sulfobetaine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.95386 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95386 Å / Relative weight: 1
ReflectionResolution: 3.51→92.6 Å / Num. obs: 37517 / % possible obs: 99.1 % / Redundancy: 3.811 % / Biso Wilson estimate: 80.215 Å2 / CC1/2: 0.989 / Rrim(I) all: 0.332 / Net I/σ(I): 5.76
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
10.47-92.63.498629.9314380.9990.03696.3
7.43-10.473.76117.8525700.9970.07699.5
6.07-7.433.81859.3933340.9860.16499.4
5.26-6.073.846.1639080.9610.2699.8
4.71-5.263.841365.3444630.950.3199.6
4.3-4.713.8344.5348940.9220.37699.6
3.98-4.33.84972.4252750.7820.72899.7
3.72-3.983.84871.4457250.6161.116399.6
3.51-3.723.77360.8259100.411.97197.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDS20190806data reduction
XDS20190806data scaling
SIMBAD2020phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.52→92.6 Å / SU ML: 0.3747 / Cross valid method: FREE R-VALUE / Phase error: 24.2127
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2551 --
Rwork0.2344 26023 -
obs-37152 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.52→92.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15762 0 0 0 15762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00316230
X-RAY DIFFRACTIONf_angle_d0.759721990
X-RAY DIFFRACTIONf_chiral_restr0.05122280
X-RAY DIFFRACTIONf_plane_restr0.00352946
X-RAY DIFFRACTIONf_dihedral_angle_d13.40385682
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.237219110802
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.188172156602
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.216134020736
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.248590835244
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.176707560279
LS refinement shellResolution: 7.32→92.6 Å
RfactorNum. reflection% reflection
Rfree0.2097 221 -
Rwork0.2098 3922 -
obs--97.57 %
Refinement TLS params.Method: refined / Origin x: -12.7585775495 Å / Origin y: -14.3865842873 Å / Origin z: 24.350387776 Å
111213212223313233
T0.695999744014 Å20.0516172626944 Å2-0.000751369513173 Å2-0.480193777922 Å2-0.111927419131 Å2--0.486855364272 Å2
L3.14342637357 °2-0.00645195763479 °2-0.00284320085977 °2--0.255136687922 °2-0.0900428333436 °2---0.22993463403 °2
S-0.204504116114 Å °-0.00377576972306 Å °-0.0251185107105 Å °-0.00474705738118 Å °0.118247231603 Å °0.00440326172949 Å °0.015987613153 Å °0.00167394911081 Å °0.00117720126662 Å °
Refinement TLS groupSelection details: all

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