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- PDB-3pgs: Phe3Gly mutant of EcFadL -

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Basic information

Entry
Database: PDB / ID: 3pgs
TitlePhe3Gly mutant of EcFadL
ComponentsLong-chain fatty acid transport protein
KeywordsLIPID TRANSPORT / beta barrel outer membrane / outer membrane
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
ACETATE ION / Long-chain fatty acid transport protein
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
Authorsvan den Berg, B. / Lepore, B.W.
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

Downloads & links

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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)99,97528
Polymers93,3542
Non-polymers6,62126
Water13,998777
1
A: Long-chain fatty acid transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,83318
Polymers46,6771
Non-polymers4,15617
Water181
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)49,14110
Polymers46,6771
Non-polymers2,4659
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.068, 147.513, 151.092
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 46676.871 Da / Num. of mol.: 2 / Fragment: Mature form (UNP Residues 26-446) / Mutation: F28G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: b2344, fadL, JW2341, ttr / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: P10384

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Non-polymers , 6 types, 803 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 777 / 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: 3.77 Å3/Da / Density % sol: 67.33 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M NaOAc pH 5.5, 8.8 w/v PEG 2000 MME. Protein dialyzed in Tris buffer, C8E4 prior to setup, 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 / Details: OXFORD DANFYSIK TOROIDAL
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8486→39 Å / Num. all: 119844 / Num. obs: 119844 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 24.3
Reflection shellResolution: 1.8486→1.88 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.818 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.818 / % possible all: 98.5

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: dev_572)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T16

1t16


Resolution: 1.9→38.778 Å / SU ML: 0.43 / σ(F): 1.34 / Phase error: 18.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1915 1834 1.66 %
Rwork0.1666 --
obs0.1671 110657 99.05 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.929 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.4925 Å20 Å20 Å2
2--4.5023 Å20 Å2
3---0.0289 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6601 0 367 777 7745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077445
X-RAY DIFFRACTIONf_angle_d1.09910048
X-RAY DIFFRACTIONf_dihedral_angle_d17.392798
X-RAY DIFFRACTIONf_chiral_restr0.084998
X-RAY DIFFRACTIONf_plane_restr0.0041305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.95140.2621340.22668216X-RAY DIFFRACTION98
1.9514-2.00880.22581330.18958191X-RAY DIFFRACTION98
2.0088-2.07360.20231390.17248258X-RAY DIFFRACTION98
2.0736-2.14770.21041410.16338236X-RAY DIFFRACTION99
2.1477-2.23370.21360.16268296X-RAY DIFFRACTION99
2.2337-2.33540.17741380.15878314X-RAY DIFFRACTION99
2.3354-2.45850.18821460.15348322X-RAY DIFFRACTION99
2.4585-2.61250.20771440.15528390X-RAY DIFFRACTION100
2.6125-2.81410.18451450.15498432X-RAY DIFFRACTION100
2.8141-3.09720.17441390.15748439X-RAY DIFFRACTION100
3.0972-3.54510.1791460.15588499X-RAY DIFFRACTION100
3.5451-4.46550.16571470.16068553X-RAY DIFFRACTION100
4.4655-38.78610.21811460.18798677X-RAY DIFFRACTION98
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)
10.8140.42410.09811.36920.42170.48370.0194-0.04530.1775-0.0109-0.04210.0298-0.12260.0330.01730.16510.0041-0.01070.1804-0.03860.1309-27.2571-4.844124.0881
22.1636-0.4685-0.61614.7742.07534.7597-0.11770.0113-0.2065-0.0770.0317-0.14490.14190.01340.08090.071-0.00830.03110.13980.00780.1442-41.4612-42.22696.0836
30.9035-0.64310.15771.2829-0.32770.50720.01090.07840.22620.0076-0.0793-0.1311-0.18140.00370.05580.2003-0.0071-0.02590.18940.05180.1618-38.0166-3.5776-22.1983
42.47050.8768-0.64426.1465-3.99286.6324-0.1166-0.0278-0.17780.0620.08790.05670.0814-0.08110.02220.05980.01940.03030.1248-0.01470.1328-23.5755-41.6607-6.656
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 1:159 or resid 195:427)
2X-RAY DIFFRACTION2chain A and resid 160:194
3X-RAY DIFFRACTION3chain B and (resid 1:159 or resid 195:425)
4X-RAY DIFFRACTION4chain B and resid 160:194

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