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- PDB-3brz: Crystal structure of the Pseudomonas putida toluene transporter TodX -

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Basic information

Entry
Database: PDB / ID: 3brz
TitleCrystal structure of the Pseudomonas 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 / SAD / Resolution: 3.2 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 1.2Feb 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
A: TodX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2605
Polymers47,0341
Non-polymers1,2264
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.302, 123.344, 167.134
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein TodX


Mass: 47034.289 Da / Num. of mol.: 1 / 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

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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: 4.29 Å3/Da / Density % sol: 71.3 %
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: X6A / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 2, 2005
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. all: 15664 / Num. obs: 15800 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 11.3 % / Rmerge(I) obs: 0.096
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.894 / Mean I/σ(I) obs: 2 / Num. unique all: 1520 / % possible all: 97.1

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.2→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3 969 -random
Rwork0.256 ---
all0.256 12786 --
obs0.256 12784 100 %-
Displacement parametersBiso mean: 83.09 Å2
Baniso -1Baniso -2Baniso -3
1--33.165 Å20 Å20 Å2
2--16.361 Å20 Å2
3---16.804 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.75 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 3.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3037 0 84 0 3121
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 (%)
3.2-3.340.4311210.3450.039158499.7
3.34-3.50.3611150.3360.034157499.9
3.5-3.70.3041200.2890.0281597100
3.7-3.950.3371270.2730.03157899.7
3.95-4.290.311130.2620.0291587100
4.29-4.790.2921180.2380.027159999.9
4.79-5.660.2571410.2140.022162099.9
5.66-80.2731140.2410.0261645100

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