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- PDB-3pgr: Asp348Arg mutant of EcFadL -

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Basic information

Entry
Database: PDB / ID: 3pgr
TitleAsp348Arg mutant of EcFadL
ComponentsLong-chain fatty acid transport protein
KeywordsLIPID TRANSPORT / beta barrel / outer membrane
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 K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLepore, B.W. / van den Berg, B. / Indic, M. / Hearn, E. / Patel, D. / Pham, H.
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
DepositionNov 2, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,86111
Polymers46,7971
Non-polymers3,06410
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.202, 65.202, 288.765
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 46797.051 Da / Num. of mol.: 1 / Mutation: D373R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: b2344, fadL, JW2341, ttr / Plasmid: pB22/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.: 10 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3.28 Å3/Da / Density % sol: 62.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: screen solution was 360mM NaCl, 0.1% w/v NaN3 15mM NaPi, 9.9% w/v PEG 4000 pH 7.0, protein dialyzed prior to setup in 10mM NaOAc, 50mM NaCl, 10% glycerol, 0.4% C8E4, pH 5.5, VAPOR DIFFUSION, ...Details: screen solution was 360mM NaCl, 0.1% w/v NaN3 15mM NaPi, 9.9% w/v PEG 4000 pH 7.0, protein dialyzed prior to setup 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: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→44 Å / Num. all: 25571 / Num. obs: 25546 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: dev_572)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T16

1t16


Resolution: 2.6→41.581 Å / SU ML: 0.95 / σ(F): 1.34 / Phase error: 24.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2599 2023 10.03 %
Rwork0.2164 --
obs0.2207 20178 99.82 %
all-25546 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.07 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.1421 Å20 Å20 Å2
2---9.1421 Å20 Å2
3---18.2842 Å2
Refinement stepCycle: LAST / Resolution: 2.6→41.581 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2924 0 136 58 3118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073208
X-RAY DIFFRACTIONf_angle_d1.094322
X-RAY DIFFRACTIONf_dihedral_angle_d17.3031191
X-RAY DIFFRACTIONf_chiral_restr0.074431
X-RAY DIFFRACTIONf_plane_restr0.004558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.66520.3591420.29841239X-RAY DIFFRACTION100
2.6652-2.73720.33491440.2661270X-RAY DIFFRACTION100
2.7372-2.81770.2891390.23731260X-RAY DIFFRACTION100
2.8177-2.90870.28821410.22211268X-RAY DIFFRACTION100
2.9087-3.01260.25771380.23761252X-RAY DIFFRACTION100
3.0126-3.13320.29121450.21761285X-RAY DIFFRACTION100
3.1332-3.27570.25861420.20351284X-RAY DIFFRACTION100
3.2757-3.44830.28181430.20431292X-RAY DIFFRACTION100
3.4483-3.66430.23151420.20861281X-RAY DIFFRACTION100
3.6643-3.9470.23421440.20961289X-RAY DIFFRACTION100
3.947-4.34380.23721460.20461319X-RAY DIFFRACTION100
4.3438-4.97150.23481450.17111312X-RAY DIFFRACTION100
4.9715-6.26010.24851500.21481350X-RAY DIFFRACTION100
6.2601-41.58630.28211620.25421454X-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)
10.5359-0.24150.27420.7435-0.52610.89340.02680.00510.03270.03880.13330.03470.0559-0.1321-0.06260.10910.0156-0.01020.31740.17250.37167.944743.5116116.1802
22.64541.336-1.0014.3520.20441.0932-0.03210.1128-0.35360.1029-0.12650.20340.3021-0.2345-0.18050.5554-0.1689-0.17480.48240.16620.42728.76373.4732139.7435
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 1:159 or resid 195:424)
2X-RAY DIFFRACTION2chain A and resid 160:194

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