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- PDB-2r8a: Crystal structure of the long-chain fatty acid transporter FadL m... -

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Basic information

Entry
Database: PDB / ID: 2r8a
TitleCrystal structure of the long-chain fatty acid transporter FadL mutant delta N8
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: 3 Å
AuthorsHearn, E.M. / Patel, D.R. / Lepore, B.W. / Indic, M. / van den Berg, B.
Citation
Journal: 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.
#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 ...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
Revision 1.3Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8306
Polymers91,6042
Non-polymers1,2264
Water00
1
A: Long-chain fatty acid transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4153
Polymers45,8021
Non-polymers6132
Water0
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)46,4153
Polymers45,8021
Non-polymers6132
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.766, 64.766, 270.651
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 45801.949 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
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM

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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: 3.15 Å3/Da / Density % sol: 60.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 10000, 8% ethylene glycol, 0.1M Hepes, pH 7.5, 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: Oct 6, 2005
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: 3→37.93 Å / Num. all: 17938 / Num. obs: 17938 / % possible obs: 80.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 13.9
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1514 / Rsym value: 0.511 / % possible all: 68.3

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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: 3→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1360 -random
Rwork0.248 ---
all0.248 21587 --
obs0.248 17357 80.4 %-
Displacement parametersBiso mean: 46.69 Å2
Baniso -1Baniso -2Baniso -3
1-12.841 Å20 Å20 Å2
2--12.841 Å20 Å2
3----25.682 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5558 0 84 0 5642
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
3-3.130.3841280.3520.034183368.5
3.13-3.290.3681390.3060.031183467.2
3.29-3.490.3471390.2810.029183168.5
3.49-3.750.291530.2630.023187469.4
3.75-4.10.3191720.260.024217479.9
4.1-4.640.2682080.2240.019252493.3
4.64-5.660.2682110.2260.018261997.8
5.66-100.2772100.2280.019266898.3

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