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- PDB-3pf1: E. coli FadL Asp348Ala mutant -

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Basic information

Entry
Database: PDB / ID: 3pf1
TitleE. coli FadL Asp348Ala mutant
ComponentsLong-chain fatty acid transport protein
KeywordsLIPID TRANSPORT / outer membrane protein / oleate / oleic / beta barrel
Function / homology
Function and homology information


long-chain fatty acid transporting porin activity / ligand-gated channel activity / cell outer membrane
Similarity search - Function
Outer membrane protein transport protein (OMPP1/FadL/TodX) / Outer membrane protein transport protein (OMPP1/FadL/TodX) / Outer membrane protein transport protein (OMPP1/FadL/TodX) / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Long-chain fatty acid transport protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsVandenberg, B. / Lepore, B.W. / Hearn, E.M. / Indic, M. / Patel, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: From the Cover: Ligand-gated diffusion across the bacterial outer membrane.
Authors: Lepore, B.W. / Indic, M. / Pham, H. / Hearn, E.M. / Patel, D.R. / van den Berg, B.
History
DepositionOct 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Long-chain fatty acid transport protein
B: Long-chain fatty acid transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,75713
Polymers92,6172
Non-polymers3,14011
Water1,62190
1
A: Long-chain fatty acid transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9937
Polymers46,3091
Non-polymers1,6856
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Long-chain fatty acid transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7646
Polymers46,3091
Non-polymers1,4555
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.880, 145.970, 151.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 1:35 or resseq 45:164 or resseq...
211chain B and (resseq 1:35 or resseq 45:164 or resseq...

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Components

#1: Protein Long-chain fatty acid transport protein / Outer membrane fadL protein / Outer membrane flp protein


Mass: 46308.555 Da / Num. of mol.: 2 / Fragment: mature form (UNP residues 26-446) / Mutation: D348A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2344, fadL, JW2341, ttr / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: P10384
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 3.75 Å3/Da / Density % sol: 67.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 15-17% PEG 4K 0.2M KCl, protein dialysed in 10mM NaOAc 50mM NaCl, 10% glycerol 0.4%C8E4, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.97981 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2008 / Details: toroidal mirror
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97981 Å / Relative weight: 1
ReflectionResolution: 2.7→47 Å / Num. all: 39050 / Num. obs: 39050 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 11.4
Reflection shellResolution: 2.7→2.95 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 4 / Rsym value: 0.514 / % possible all: 98.4

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIXmodel building
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T16

1t16


Resolution: 2.7→41.48 Å / SU ML: 1.06
Isotropic thermal model: TLS-derived anisotropic protein, isotropic ligands and solvent
σ(F): 1.34 / Phase error: 25.85 / Stereochemistry target values: ML
Details: RMS average Biso for solvent/ligands. Anisotropic scale factor is reported as Anisotropic B
RfactorNum. reflection% reflection
Rfree0.2727 1983 5.08 %
Rwork0.2104 --
obs0.2135 39025 99.85 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.676 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--12.7105 Å2-0 Å2-0 Å2
2---2.6325 Å2-0 Å2
3----4.5689 Å2
Refinement stepCycle: LAST / Resolution: 2.7→41.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6558 0 165 90 6813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086936
X-RAY DIFFRACTIONf_angle_d1.1339361
X-RAY DIFFRACTIONf_dihedral_angle_d16.8522480
X-RAY DIFFRACTIONf_chiral_restr0.073944
X-RAY DIFFRACTIONf_plane_restr0.0051220
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3058X-RAY DIFFRACTIONPOSITIONAL
12B3058X-RAY DIFFRACTIONPOSITIONAL0.029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.76750.43751440.34062584X-RAY DIFFRACTION99
2.7675-2.84230.35161500.28672609X-RAY DIFFRACTION100
2.8423-2.9260.36461280.2442599X-RAY DIFFRACTION100
2.926-3.02040.26831330.21932619X-RAY DIFFRACTION100
3.0204-3.12830.28941530.19372605X-RAY DIFFRACTION100
3.1283-3.25350.26581390.18922599X-RAY DIFFRACTION100
3.2535-3.40150.27751460.19622626X-RAY DIFFRACTION100
3.4015-3.58070.29371410.19882610X-RAY DIFFRACTION100
3.5807-3.80490.27321450.20922640X-RAY DIFFRACTION100
3.8049-4.09850.26211250.19972688X-RAY DIFFRACTION100
4.0985-4.51050.21711340.17182655X-RAY DIFFRACTION100
4.5105-5.16210.20441510.16792666X-RAY DIFFRACTION100
5.1621-6.49970.27441440.22672704X-RAY DIFFRACTION100
6.4997-41.48480.26211500.24792838X-RAY DIFFRACTION99
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)
10.44080.32680.04040.60130.15630.3153-0.0364-0.05030.1075-0.0109-0.03880.0844-0.1379-0.03990.0620.04980.0072-0.03610.0928-0.03950.0917-26.1941-5.901821.0332
20.4572-0.29030.00680.373-0.10750.2254-0.0256-0.05160.2363-0.0398-0.019-0.1317-0.1394-0.00160.01880.0739-0.02050.01330.06360.05980.1006-34.8391-7.602-23.0012
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 1:424)
2X-RAY DIFFRACTION2chain B and (resid 1:424)

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