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- PDB-2r88: Crystal structure of the long-chain fatty acid transporter FadL m... -

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Basic information

Entry
Database: PDB / ID: 2r88
TitleCrystal structure of the long-chain fatty acid transporter FadL mutant delta S3 kink
ComponentsLong-chain fatty acid transport protein
KeywordsTRANSPORT PROTEIN / beta barrel / outer membrane protein / Lipid transport / Phage recognition / Transmembrane / Transport
Function / homology
Function and homology information


long-chain fatty acid transporting porin activity / ligand-gated channel activity / long-chain fatty acid transport / 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: 2.6 Å
AuthorsHearn, E.M. / Patel, D.R. / Lepore, B.W. / Indic, M. / van den Berg, B.
Citation
Journal: Nature / Year: 2009
Title: Transmembrane passage of hydrophobic compounds through a protein channel wall
Authors: Hearn, E.M. / Patel, D.R. / Lepore, B.W. / Indic, M. / van den Berg, B.
#1: Journal: Science / Year: 2004
Title: Crystal structure of the long-chain fatty acid transporter FadL
Authors: van den Berg, B. / Black, P.N. / Clemons Jr., W.M. / Rapoport, T.A.
History
DepositionSep 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)93,2682
Polymers93,2682
Non-polymers00
Water00
1
A: Long-chain fatty acid transport protein


Theoretical massNumber of molelcules
Total (without water)46,6341
Polymers46,6341
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Long-chain fatty acid transport protein


Theoretical massNumber of molelcules
Total (without water)46,6341
Polymers46,6341
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.327, 91.370, 267.317
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 46633.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fadL, ttr / Plasmid: pBAD22 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P10384
Sequence detailsSEQUENCE RESIDUES S100, N101, Y102, AND G103 WERE REPLACED WITH RESIDUES ALA, ASN, AND ASP TO FORM ...SEQUENCE RESIDUES S100, N101, Y102, AND G103 WERE REPLACED WITH RESIDUES ALA, ASN, AND ASP TO FORM THE DELTA S3 KINK.

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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: 3.04 Å3/Da / Density % sol: 59.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 5000 MME, 0.2M ammonium sulfate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 22, 2007
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.55→31.9 Å / Num. obs: 33965 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.3 / Redundancy: 8.9 % / Biso Wilson estimate: 47.5 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.9
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3041 / Rsym value: 0.563 / % possible all: 84.2

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T16

1t16


Resolution: 2.6→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1618 -RANDOM
Rwork0.262 ---
all0.262 ---
obs0.262 31548 92.3 %-
Displacement parametersBiso mean: 49.67 Å2
Baniso -1Baniso -2Baniso -3
1-9.35 Å20 Å20 Å2
2--8.86 Å20 Å2
3----18.206 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5624 0 0 0 5624
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.4
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.6-2.720.4091770.3390.031366486.6
2.72-2.860.2891720.2930.022372788.1
2.86-3.030.3382120.3170.023374188.8
3.03-3.260.3441910.290.025374587.6
3.26-3.570.3151970.2680.022378889.1
3.57-4.060.2912330.2640.019416997.5
4.06-50.2682090.240.019431599.9
5-100.2612270.2320.0174399100

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