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- PDB-2r4n: Crystal structure of the long-chain fatty acid transporter FadL m... -

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Basic information

Entry
Database: PDB / ID: 2r4n
TitleCrystal structure of the long-chain fatty acid transporter FadL mutant N33A
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: 3.2 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)93,8834
Polymers93,4242
Non-polymers4592
Water00
1
A: Long-chain fatty acid transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9412
Polymers46,7121
Non-polymers2291
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)46,9412
Polymers46,7121
Non-polymers2291
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.206, 39.986, 174.996
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 46711.918 Da / Num. of mol.: 2 / Mutation: N33A, I197T
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.: 2 / 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: 2.68 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 295 K / pH: 4.6
Details: 30% PEG 400, 0.1M cadmium chloride, 0.1M sodium acetate, pH 4.60, 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 4, 2006
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: 3.11→37.12 Å / Num. obs: 15295 / % possible obs: 85.1 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 6.8
Reflection shellResolution: 3.11→3.21 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 3.78 / Rsym value: 0.288 / % possible all: 76.9

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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: 3.2→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.332 1049 -RANDOM
Rwork0.235 ---
obs0.235 13667 85.2 %-
Displacement parametersBiso mean: 22.97 Å2
Baniso -1Baniso -2Baniso -3
1-6.016 Å20 Å20 Å2
2---16.244 Å20 Å2
3---10.228 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.72 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 3.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6498 0 32 0 6530
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_deg1.6
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: 3.2→3.34 Å / Rfactor Rfree error: 0.034
RfactorNum. reflection% reflection
Rfree0.393 133 -
Rwork0.287 --
obs--79.5 %

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