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- PDB-6z37: TodX monoaromatic hydrocarbon channel deltaS2 mutant -

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Basic information

Entry
Database: PDB / ID: 6z37
TitleTodX monoaromatic hydrocarbon channel deltaS2 mutant
ComponentsTodX
KeywordsMEMBRANE PROTEIN / FadL monoaromatic hydrocarbons biodegradation toluene outer membrane transport diffusion TodX
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: 3.05 Å
Authorsvan den Berg, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM104495-01 United States
CitationJournal: Nat Commun / Year: 2020
Title: Uptake of monoaromatic hydrocarbons during biodegradation by FadL channel-mediated lateral diffusion.
Authors: Somboon, K. / Doble, A. / Bulmer, D. / Basle, A. / Khalid, S. / van den Berg, B.
History
DepositionMay 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TodX


Theoretical massNumber of molelcules
Total (without water)46,2951
Polymers46,2951
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.126, 116.543, 170.068
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein TodX


Mass: 46295.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: todX / Production host: Escherichia coli (E. coli) / References: UniProt: Q51971, UniProt: A5W4F4*PLUS

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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: 71.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Na-citrate (pH 3.5), 0.2 M Li2SO4, 28% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.05→48.07 Å / Num. obs: 15557 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 105.13 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.034 / Net I/σ(I): 11.5
Reflection shellResolution: 3.05→3.26 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 2777 / CC1/2: 0.935 / Rpim(I) all: 0.2

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BRZ

3brz


Resolution: 3.05→48.07 Å / SU ML: 0.4506 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 32.9127
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2983 776 4.99 %
Rwork0.2314 14769 -
obs0.2347 15545 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 128.38 Å2
Refinement stepCycle: LAST / Resolution: 3.05→48.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3146 0 0 0 3146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00963209
X-RAY DIFFRACTIONf_angle_d1.3384355
X-RAY DIFFRACTIONf_chiral_restr0.0744491
X-RAY DIFFRACTIONf_plane_restr0.0063564
X-RAY DIFFRACTIONf_dihedral_angle_d7.161858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.240.36811270.29242416X-RAY DIFFRACTION99.88
3.24-3.490.28431400.25582402X-RAY DIFFRACTION99.88
3.49-3.840.35861270.23212431X-RAY DIFFRACTION99.84
3.84-4.40.30871180.21592467X-RAY DIFFRACTION100
4.4-5.540.27631250.22032476X-RAY DIFFRACTION99.92
5.54-48.070.28911390.23362577X-RAY DIFFRACTION99.96
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)
13.741940779130.3482800679651.461263063250.832407712357-0.08920261046450.645014945234-0.420738509033-0.5370433021260.416634062047-0.972555147409-0.0153543132658-0.580483025418-0.07593354886661.059718604780.0630511925460.701347895937-0.1437748031630.5318416554931.3389826376-0.8036337985361.478162299268.6253374284830.0362914701210.155002379
22.398702712390.126718311179-1.099048408324.298506068812.239534591144.23976476953-0.0736324563662-0.3090256826160.5319086225-0.3329695481150.414884468055-0.294337198114-0.1195727524160.252389166956-0.395741137610.806711305426-0.1762396707320.04801230572210.744207744001-0.241143679020.82285830401211.69666576719.8959856455194.671114075
31.81815471798-0.713457134299-1.000743871562.68332360592.671862539795.83241881288-0.0577845668006-0.08660936704110.3801312420580.145996586228-0.3121619964310.272419476533-0.019234626286-1.037402069830.26179432250.854479629896-0.1045918530410.05040935092450.816591640721-0.2121318064040.9446351208461.049661937422.8136734415203.228914124
40.7371812852520.723349032488-0.3711916442521.18306434414-0.6205609408590.380561943925-0.1000485628210.233524762606-0.0563334685723-0.3600644295311.42636319859-0.4643426815760.01010972666240.632889588393-0.8640298413021.06431964291-0.0368460850911-0.0009713518527381.06058292138-0.3645797316970.9150228220857.4172363852713.7737170684194.5743072
51.435460185980.2456489729360.9044830565214.432695480984.048053628357.12943297180.0769470813359-0.4502454549020.432009033271-0.169951476758-0.3619564810590.4273465507010.110721206003-0.6844498965350.2941282536271.12826433240.1675712264410.1627834411921.01302499628-0.2253587376730.8486452399335.5762832664318.8449175011209.273037019
62.65504629440.009878128848921.503409651713.128299636941.548748500694.49026503681-0.0210628248206-0.7839818641710.8172826843490.6679921092670.760658837077-0.3551577084470.2204540182170.901732902054-0.5639543390230.9339176879390.1634379799250.1128567022331.17042481408-0.45905791.0236656764411.548973550120.2673634572207.82884625
70.432405405622-0.6392793589340.5405840528112.212962731961.750835905893.486554464010.478031061484-1.560517506010.9602707967540.7849616283720.263863719773-0.5599249868330.4546978466430.734185977775-0.739366697181.08206212777-0.2426422794450.3377224945761.33066007016-0.7695700810231.5338451244917.833936346623.5503422122206.613351769
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 33 )
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 208 )
3X-RAY DIFFRACTION3chain 'A' and (resid 209 through 251 )
4X-RAY DIFFRACTION4chain 'A' and (resid 252 through 282 )
5X-RAY DIFFRACTION5chain 'A' and (resid 283 through 310 )
6X-RAY DIFFRACTION6chain 'A' and (resid 311 through 351 )
7X-RAY DIFFRACTION7chain 'A' and (resid 352 through 428 )

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