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- PDB-3poq: Crystal structure of E.coli OmpF porin in lipidic cubic phase: sp... -

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Basic information

Entry
Database: PDB / ID: 3poq
TitleCrystal structure of E.coli OmpF porin in lipidic cubic phase: space group H32, small unit cell
ComponentsOmpF protein
KeywordsMEMBRANE PROTEIN / beta barrel / solute transport / pore
Function / homology
Function and homology information


colicin transmembrane transporter activity / porin activity / monoatomic ion channel complex / pore complex / protein homotrimerization / monoatomic ion channel activity / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / protein transport ...colicin transmembrane transporter activity / porin activity / monoatomic ion channel complex / pore complex / protein homotrimerization / monoatomic ion channel activity / lipopolysaccharide binding / cell outer membrane / 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. / Porin domain, Gram-negative type / Gram-negative porin / Porin, Gram-negative type / Porin / : / Porin domain superfamily / Porin ...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
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / THIOCYANATE ION / : / Outer membrane porin F
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsEfremov, R.G. / Sazanov, L.A.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Structure of Escherichia coli OmpF porin from lipidic mesophase.
Authors: Efremov, R.G. / Sazanov, L.A.
History
DepositionNov 23, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references
Revision 1.2Nov 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: OmpF protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,48927
Polymers37,1141
Non-polymers8,37526
Water3,297183
1
A: OmpF protein
hetero molecules

A: OmpF protein
hetero molecules

A: OmpF protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,46781
Polymers111,3433
Non-polymers25,12478
Water543
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 area8650 Å2
ΔGint-56 kcal/mol
Surface area40350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.310, 77.310, 330.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-384-

HOH

21A-389-

HOH

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Components

#1: Protein OmpF protein / Outer membrane protein F


Mass: 37114.250 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 23-362 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: BL21 / References: UniProt: C5W2U9, UniProt: P02931*PLUS
#2: Chemical...
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.56 Å3/Da / Density % sol: 51.95 % / Description: THE FILE CONTAINS FRIEDEL PAIRS. / Mosaicity: 0.65 °
Crystal growTemperature: 296 K / pH: 4.6
Details: 0.1M sodium acetate, 2.7M lithium nitrate, 2.0M potassium thiocyanate, pH 4.6, lipidic sponge phase, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Date: Nov 24, 2009 / Details: mirrors
RadiationMonochromator: LN2 cooled fixed exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→19.352 Å / Num. all: 27555 / Num. obs: 27555 / % possible obs: 91.2 % / Redundancy: 4.6 % / Biso Wilson estimate: 19.22 Å2 / Rmerge(I) obs: 0.172 / Rsym value: 0.155 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.9-23.90.4940.431.71631341660.2370.4940.432.495.3
2-2.123.90.3840.3342.11530039220.1840.3840.3343.294.3
2.12-2.274.20.3110.2742.61494235710.1410.3110.2744.391.9
2.27-2.454.60.2680.2382.61552133650.1180.2680.2385.193.2
2.45-2.6950.2130.1933.71534830710.0880.2130.1936.791.1
2.69-34.70.1780.1614.31259126560.0750.1780.161887.9
3-3.475.50.150.1384.61298823680.0580.150.13810.788.1
3.47-4.2550.1390.1264.7984119850.0580.1390.12611.485.9
4.25-6.015.40.1190.1085.3859515900.0490.1190.10812.288.9
6.01-19.3525.10.0970.088644248610.0390.0970.08811.583.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.5 Å29.93 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.1.4phasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
RemDAqdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OMF

2omf


Resolution: 1.9→19.352 Å / WRfactor Rwork: 0.2792 / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.29 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.72 / Stereochemistry target values: ML / Details: THE FILE CONTAINS FRIEDEL PAIRS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1376 5 %random
Rwork0.2269 ---
obs0.2295 27547 90 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.794 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso max: 64.43 Å2 / Biso min: 8.63 Å2
Baniso -1Baniso -2Baniso -3
1--6.6034 Å20 Å20 Å2
2---6.6034 Å20 Å2
3---13.2067 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2627 0 228 183 3038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092885
X-RAY DIFFRACTIONf_angle_d1.1443806
X-RAY DIFFRACTIONf_dihedral_angle_d12.2651088
X-RAY DIFFRACTIONf_chiral_restr0.074368
X-RAY DIFFRACTIONf_plane_restr0.005490
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.96790.33541310.293273695
1.9679-2.04660.3291480.268269094
2.0466-2.13960.31141400.2563263793
2.1396-2.25230.3241410.2519261191
2.2523-2.39310.32391500.2519264992
2.3931-2.57750.29281640.2399262491
2.5775-2.83620.29891310.2409252487
2.8362-3.24490.28631210.2288254687
3.2449-4.08190.21881320.1909250885
4.0819-19.35280.23871180.1953264685

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