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- PDB-3bs0: Crystal structure of the P. putida toluene transporter TodX -

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Basic information

Entry
Database: PDB / ID: 3bs0
TitleCrystal structure of the P. putida toluene transporter TodX
ComponentsTodX
KeywordsTRANSPORT PROTEIN / beta barrel / outer membrane protein
Function / homology
Function and homology information


long-chain fatty acid transporting porin 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
Membrane protein involved in aromatic hydrocarbon degradation / TodX
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHearn, E.M. / Patel, D.R. / van den Berg, B.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Outer-membrane transport of aromatic hydrocarbons as a first step in biodegradation.
Authors: Hearn, E.M. / Patel, D.R. / van den Berg, B.
History
DepositionDec 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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: TodX
B: TodX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2946
Polymers94,0692
Non-polymers1,2264
Water1,58588
1
A: TodX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6473
Polymers47,0341
Non-polymers6132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TodX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6473
Polymers47,0341
Non-polymers6132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.098, 41.415, 141.064
Angle α, β, γ (deg.)98.39, 90.01, 90.06
Int Tables number1
Space group name H-MP1

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Components

#1: Protein TodX


Mass: 47034.289 Da / Num. of mol.: 2 / Fragment: sequence database residues 21-453
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: F1 / Gene: todX / Plasmid: pBAD22 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q51971, UniProt: A5W4F4*PLUS
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


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


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.34 Å3/Da / Density % sol: 47.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 25% PEG 4000, 0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2005
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: 2.5→46.52 Å / Num. all: 26096 / Num. obs: 26096 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 2.8 % / Biso Wilson estimate: 53.6 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 18.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 3 / Num. unique all: 2115 / % possible all: 71.2

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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 3BRZ

3brz


Resolution: 2.6→11.98 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.291 1189 -RANDOM
Rwork0.253 ---
all0.253 25967 --
obs0.253 23644 91.1 %-
Displacement parametersBiso mean: 52.51 Å2
Baniso -1Baniso -2Baniso -3
1-10.8 Å22.14 Å20 Å2
2--7.13 Å210.42 Å2
3----17.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.6→11.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6238 0 84 88 6410
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.9
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.6-2.720.3691450.3630.031275583.7
2.72-2.860.3841390.3290.033282189.3
2.86-3.030.341610.2780.027294189.6
3.03-3.260.3761360.2820.032295090.8
3.26-3.590.3121460.2520.026297891.6
3.59-4.090.2641500.230.022305894.1
4.09-5.080.2271600.2110.018307894.2
5.08-11.980.2911520.2620.024306394.6

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