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- PDB-3dwo: Crystal structure of a Pseudomonas aeruginosa FadL homologue -

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Basic information

Entry
Database: PDB / ID: 3dwo
TitleCrystal structure of a Pseudomonas aeruginosa FadL homologue
ComponentsProbable outer membrane protein
KeywordsMEMBRANE PROTEIN / beta barrel / outer membrane protein
Function / homology: / long-chain fatty acid transporting porin activity / 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 / Probable outer membrane protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 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
DepositionJul 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Probable outer membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,38013
Polymers48,9131
Non-polymers3,46712
Water3,855214
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.777, 233.054, 81.899
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Probable outer membrane protein


Mass: 48913.176 Da / Num. of mol.: 1 / Fragment: UNP residues 22-463
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA4589 / Plasmid: pBAD22 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q9HVJ6
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.77 Å3/Da / Density % sol: 55.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 28-32% PEG 400, 0.1M lithium sulfate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9790, 1.0375, 1.1397
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 29, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21.03751
31.13971
ReflectionResolution: 2.1→50 Å / Num. all: 31016 / Num. obs: 28897 / % possible obs: 89.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.4 / Redundancy: 5.6 % / Rmerge(I) obs: 0.073 / Net I/av σ(I): 20.4 / Net I/σ(I): 10
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1218 / Rsym value: 0.287 / % possible all: 38.6

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→20 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1358 4.8 %random
Rwork0.213 ---
all0.213 28103 --
obs0.213 26996 96.1 %-
Solvent computationBsol: 65.517 Å2
Displacement parametersBiso max: 79 Å2 / Biso mean: 33.501 Å2 / Biso min: 13.37 Å2
Baniso -1Baniso -2Baniso -3
1-2.415 Å20 Å20 Å2
2--1.48 Å20 Å2
3----3.895 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3386 0 136 214 3736
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.369
X-RAY DIFFRACTIONc_mcbond_it1.2951.5
X-RAY DIFFRACTIONc_scbond_it2.1852
X-RAY DIFFRACTIONc_mcangle_it2.0232
X-RAY DIFFRACTIONc_scangle_it3.2542.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5c8e4.parc8e4.top

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