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- PDB-3pgu: Phe3Glu mutant of EcFadL -

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Basic information

Entry
Database: PDB / ID: 3pgu
TitlePhe3Glu mutant of EcFadL
ComponentsLong-chain fatty acid transport protein
KeywordsLIPID TRANSPORT / outer membrane 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
NICKEL (II) ION / OLEIC ACID / Long-chain fatty acid transport protein
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLepore, B.W. / Indic, M. / Pham, H. / Hearn, E. / Patel, D. / van den Berg, B.
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 1.2Jan 7, 2015Group: Structure summary
Revision 1.3Sep 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,72823
Polymers46,7491
Non-polymers5,97922
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.200, 65.200, 280.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-486-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 46748.938 Da / Num. of mol.: 1 / Fragment: mature form (UNP residues 26-446) / Mutation: F28E
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, 268 molecules

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


Mass: 306.438 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 3.19 Å3/Da / Density % sol: 61.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15mM tricine pH 8.5 24% w/v PEG 4000, prior to setup, protein dialyzed in Tris, NaCl pH8 C8E4, 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 315 / Detector: CCD / Date: Apr 26, 2010 / Details: mirrors
RadiationMonochromator: Si(111)channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.5→44 Å / Num. all: 98214 / Num. obs: 92723 / % possible obs: 86.64 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 7.6
Reflection shellResolution: 1.5→1.79 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 4.4 / Rsym value: 0.497 / % possible all: 97.1

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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: 1.7→42.506 Å / SU ML: 0.4 / σ(F): 1.35 / Phase error: 15.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1802 3448 2.72 %
Rwork0.1675 --
obs0.1679 126635 99.7 %
all-98214 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.829 Å2 / ksol: 0.391 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.5517 Å2-0 Å20 Å2
2---4.5517 Å20 Å2
3---4.5084 Å2
Refinement stepCycle: LAST / Resolution: 1.7→42.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3165 0 287 246 3698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063792
X-RAY DIFFRACTIONf_angle_d1.0855084
X-RAY DIFFRACTIONf_dihedral_angle_d15.721472
X-RAY DIFFRACTIONf_chiral_restr0.084494
X-RAY DIFFRACTIONf_plane_restr0.004657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72330.22641460.22274935X-RAY DIFFRACTION100
1.7233-1.74790.22331550.21024945X-RAY DIFFRACTION100
1.7479-1.7740.19341410.18914951X-RAY DIFFRACTION100
1.774-1.80170.1871180.17854943X-RAY DIFFRACTION100
1.8017-1.83130.22081750.1784889X-RAY DIFFRACTION100
1.8313-1.86280.20351300.1694978X-RAY DIFFRACTION100
1.8628-1.89670.20681400.16464897X-RAY DIFFRACTION100
1.8967-1.93320.18761220.16224962X-RAY DIFFRACTION100
1.9332-1.97270.20111170.1534982X-RAY DIFFRACTION100
1.9727-2.01560.20491190.15624901X-RAY DIFFRACTION100
2.0156-2.06240.19381480.15854949X-RAY DIFFRACTION100
2.0624-2.1140.17711300.15054950X-RAY DIFFRACTION100
2.114-2.17120.13491240.1484980X-RAY DIFFRACTION100
2.1712-2.23510.14791290.14044929X-RAY DIFFRACTION100
2.2351-2.30720.15281360.1534945X-RAY DIFFRACTION100
2.3072-2.38960.18471530.15384890X-RAY DIFFRACTION100
2.3896-2.48530.17691530.15384939X-RAY DIFFRACTION100
2.4853-2.59840.15411420.16154898X-RAY DIFFRACTION100
2.5984-2.73540.18811630.15984888X-RAY DIFFRACTION99
2.7354-2.90670.18021230.15844937X-RAY DIFFRACTION100
2.9067-3.13110.18461460.16914921X-RAY DIFFRACTION99
3.1311-3.44610.1461280.16654928X-RAY DIFFRACTION99
3.4461-3.94440.16741460.17014896X-RAY DIFFRACTION99
3.9444-4.96830.16261430.16234877X-RAY DIFFRACTION99
4.9683-42.51930.23831210.22494877X-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)
10.25-0.1362-0.03050.10950.12960.4958-0.0003-0.00490.00680.01870.0019-0.0062-0.0193-0.0177-0.01030.063-0.0019-0.00010.10030.06960.11-24.394719.3152-33.007
20.16950.1818-0.14850.6125-0.2970.3160.05180.01010.02890.07420.02640.0183-0.0479-0.04040.05440.0597-0.00010.00390.08630.10890.0747-19.58839.7125-23.8485
30.1306-0.04920.04990.34-0.26530.29540.0399-0.0027-0.0197-0.0236-0.0055-0.01270.0794-0.01140.04270.1163-0.0074-0.02820.08720.08190.0977-21.216-5.7518-23.4121
40.04850.05990.04970.09760.14490.3430.04360.0181-0.0181-0.0541-0.0159-0.19010.15210.1269-00.09610.0279-0.00350.11760.07520.2097-16.00861.6169-35.8536
50.494-0.48740.12920.7801-0.21410.40270.03090.01260.0389-0.0413-0.0082-0.01830.0171-0.0352-0.00680.03560.00540.00070.07880.07280.1092-33.221715.9394-31.8764
64.4728-4.7151.03335.3028-1.16510.3780.17430.1743-0.2407-0.203-0.05050.23460.0844-0.0554-0.12020.1363-0.0052-0.01090.11530.03780.2059-24.2738-14.0728-27.0054
70.68810.72630.03932.0770.36790.61540.0698-0.02390.04510.1265-0.03260.0493-0.0199-0.0329-0.00950.04340.01130.01960.06050.06410.0935-32.063222.1864-24.0122
80.5770.6641-0.1332.4806-0.31320.0638-0.00350.0017-0.005-0.06020.07930.15210.0304-0.0307-0.06810.12220.0023-0.01970.12950.06120.1193-28.381311.3664-20.8797
90.53070.349-0.11861.07380.03050.27780.05330.01830.060.10870.05570.0899-0.0477-0.0546-0.00120.05570.0047-0.01490.080.07970.0839-24.272812.998-19.4984
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:43)
2X-RAY DIFFRACTION2chain 'A' and (resseq 44:99)
3X-RAY DIFFRACTION3chain 'A' and (resseq 100:218)
4X-RAY DIFFRACTION4chain 'A' and (resseq 219:266)
5X-RAY DIFFRACTION5chain 'A' and (resseq 267:298)
6X-RAY DIFFRACTION6chain 'A' and (resseq 299:321)
7X-RAY DIFFRACTION7chain 'A' and (resseq 322:349)
8X-RAY DIFFRACTION8chain 'A' and (resseq 350:380)
9X-RAY DIFFRACTION9chain 'A' and (resseq 381:425)

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