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- PDB-3bry: Crystal structure of the Ralstonia pickettii toluene transporter TbuX -

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Basic information

Entry
Database: PDB / ID: 3bry
TitleCrystal structure of the Ralstonia pickettii toluene transporter TbuX
ComponentsTbuX
KeywordsTRANSPORT PROTEIN / beta barrel / outer membrane protein
Function / homologyOuter membrane protein transport protein (OMPP1/FadL/TodX) / long-chain fatty acid transporting porin activity / Outer membrane protein transport protein (OMPP1/FadL/TodX) / Outer membrane protein transport protein (OMPP1/FadL/TodX) / Porin / cell outer membrane / Beta Barrel / Mainly Beta / Aromatic hydrocarbon degradation protein
Function and homology information
Biological speciesRalstonia pickettii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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: TbuX
B: TbuX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,1664
Polymers92,5532
Non-polymers6132
Water00
1
A: TbuX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5832
Polymers46,2771
Non-polymers3061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TbuX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5832
Polymers46,2771
Non-polymers3061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.291, 125.244, 269.511
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

#1: Protein TbuX


Mass: 46276.641 Da / Num. of mol.: 2 / Fragment: sequence database residues 26-458
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia pickettii (bacteria) / Strain: PKO1 / Gene: tbuX / Plasmid: pBAD22 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q9RBW8
#2: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 2 / 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: 2.86 Å3/Da / Density % sol: 56.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% PEG 4000, 0.1 M magnesium acetate, 50 mM sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9198 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 22, 2006
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 2.74→31.92 Å / Num. all: 27405 / Num. obs: 27405 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.076
Reflection shellResolution: 2.74→2.85 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 2.1 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The starting model was a partial structure of TbuX that was determined from a SAD dataset but did not refine well.
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1255 -random
Rwork0.268 ---
all0.268 16516 --
obs0.268 25331 98.4 %-
Displacement parametersBiso mean: 47.29 Å2
Baniso -1Baniso -2Baniso -3
1--4.54 Å20 Å20 Å2
2---4.512 Å20 Å2
3---9.052 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 3.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5666 0 42 0 5708
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.8
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
3.2-3.340.3291630.2950.026202799.2
3.34-3.50.2531650.2680.02202899.1
3.5-3.70.2461520.2480.02204698.7
3.7-3.950.2871430.2560.024201298.8
3.95-4.290.2871270.2650.026202798.4
4.29-4.790.2571610.2330.02207598
4.79-5.660.2821880.2760.021202697.5
5.66-80.3141560.3230.025204496.7

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