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- PDB-2r4o: Crystal structure of the long-chain fatty acid transporter FadL m... -

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Basic information

Entry
Database: PDB / ID: 2r4o
TitleCrystal structure of the long-chain fatty acid transporter FadL mutant delta NPA
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: 3.6 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
DepositionAug 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)94,2056
Polymers93,2882
Non-polymers9184
Water00
1
A: Long-chain fatty acid transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1033
Polymers46,6441
Non-polymers4592
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)47,1033
Polymers46,6441
Non-polymers4592
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.050, 146.618, 151.227
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 46643.801 Da / Num. of mol.: 2 / Mutation: N33G,P33G,A33G
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-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, 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: 3.81 Å3/Da / Density % sol: 67.75 %
Crystal growTemperature: 295 K / pH: 5.5
Details: 35% PEG 2000, 0.05M magnesium acetate, 0.05M cacodylate, pH 5.50, 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
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 17, 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: 3.6→41.54 Å / Num. obs: 16885 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.287 / Net I/σ(I): 3.1
Reflection shellResolution: 3.6→3.73 Å / Redundancy: 4 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.593 / % possible all: 97

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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: 3.6→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.314 1602 -RANDOM
Rwork0.243 ---
obs0.243 15827 98.7 %-
all-16034 --
Displacement parametersBiso mean: 12.86 Å2
Baniso -1Baniso -2Baniso -3
1-15.153 Å20 Å20 Å2
2---14.122 Å20 Å2
3----1.031 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.83 Å0.68 Å
Refinement stepCycle: LAST / Resolution: 3.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6488 0 64 0 6552
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.55
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.6→3.76 Å / Rfactor Rfree error: 0.027
RfactorNum. reflection% reflection
Rfree0.379 196 -
Rwork0.319 --
obs--97.1 %

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