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- PDB-6z38: TodX deltaS2S3 mutant monoaromatic hydrocarbon channel -

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Basic information

Entry
Database: PDB / ID: 6z38
TitleTodX deltaS2S3 mutant monoaromatic hydrocarbon channel
ComponentsTodX
KeywordsMEMBRANE PROTEIN / FadL monoaromatic hydrocarbons biodegradation toluene outer membrane transport diffusion TodX
Function / homologylong-chain fatty acid transporting porin activity / Outer membrane protein transport protein (OMPP1/FadL/TodX) / Outer membrane protein transport protein (OMPP1/FadL/TodX) / membrane / TodX
Function and homology information
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 9, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Dec 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 1.3Jan 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)46,2641
Polymers46,2641
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 area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.107, 115.928, 172.807
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: 46264.477 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

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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: 4.34 Å3/Da / Density % sol: 71.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.05 M Na-citrate (pH 4.5), 0.1 M Li2SO4, 30% 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: 2.9→48.14 Å / Num. obs: 18258 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 96.18 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.034 / Net I/σ(I): 13.2
Reflection shellResolution: 2.9→3.08 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2917 / CC1/2: 0.58 / Rpim(I) all: 0.58

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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: 2.9→48.14 Å / SU ML: 0.5472 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.7724
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3175 863 4.73 %
Rwork0.2529 17389 -
obs0.2558 18252 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 127.48 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3115 0 0 0 3115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00963177
X-RAY DIFFRACTIONf_angle_d1.33014313
X-RAY DIFFRACTIONf_chiral_restr0.0679488
X-RAY DIFFRACTIONf_plane_restr0.0063558
X-RAY DIFFRACTIONf_dihedral_angle_d5.55521840
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.080.46941340.34992871X-RAY DIFFRACTION99.97
3.08-3.320.42821570.31592836X-RAY DIFFRACTION100
3.32-3.650.37691120.26542886X-RAY DIFFRACTION100
3.65-4.180.28291550.23592868X-RAY DIFFRACTION99.97
4.18-5.270.27631470.23412913X-RAY DIFFRACTION100
5.27-48.140.31551580.24863015X-RAY DIFFRACTION99.91
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)
10.1316001354420.7941424671960.1285599761464.406967641711.368913566125.11725370073-0.447089138072-1.614396129371.12349276755-1.18963971224-0.1776153513180.3316742830360.02380615839670.4355668371210.1282907174220.771761833415-0.125685439970.3043268241221.05621685016-0.8353087057341.099433965027.0466467603932.1477944293214.092940607
22.02639561502-1.53273270249-0.5356254601914.994559827991.566847940984.097030714170.0181338516158-0.1904076155920.9762059001580.2705937894450.49790760026-1.34877498185-0.1216357417340.521472415082-0.09491324403830.861139245987-0.0758013698293-0.04520208453080.783079406443-0.3182846825870.86025507953114.396370700327.4282633401202.936656679
31.269768133231.687607049570.0295213676973.123376380942.082238532114.19872956255-0.1874127344720.143754037076-0.0825521553496-0.6718369607240.250157079487-0.334697750040.208583924685-0.01880515264150.01174815662360.614641822609-0.1330806743040.1092702996150.445095135167-0.1595776353330.58420593169611.062337823713.0366241826193.007612059
40.4055848521580.2918971190840.4506936457112.771931915051.539104092141.498192458530.0819502590464-0.07433059548590.624713079185-0.02004812209340.3847019487430.1741322762730.0729014971563-0.07498032198920.09690537277140.655746483-0.07120102285120.147552965920.880796141537-0.3828587599260.9476969728444.4051202170220.1654707112204.697422978
51.18076064010.2866539843930.8683527013683.390615009063.879484851868.586633023860.0342087175603-0.01965921108810.139449259602-0.01212395799-0.1450293266080.2630452756840.745109106553-0.330615988782-0.07516455080950.8681647248720.272325107057-0.02947031214670.744442669234-0.1217940757790.6144165619595.7892392217113.7457670563206.417063022
60.41874139144-0.7276720496380.7732371293971.06278687571-0.6417129696894.162336894710.0534962532488-1.169118850780.3464849674151.763383356640.362928625101-0.3019200883640.3066742350490.228391932632-0.107358664250.982318696538-0.4512496392540.3660750532921.24518598635-0.8740127988161.4487712714217.376826973226.7400000267214.263569948
70.279351082895-0.451388743393-0.7949084458445.808373833832.193149390812.11443219661-0.251016072131-1.272276090220.05547261762140.4455024133361.15928443698-0.9158948851150.6521327502531.54061344217-0.6005735231891.11748072492-0.0818946737355-0.1623073301851.19785161581-0.4822867710081.2099458893220.318302245821.8147000288208.034920724
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 103 )
3X-RAY DIFFRACTION3chain 'A' and (resid 104 through 207 )
4X-RAY DIFFRACTION4chain 'A' and (resid 208 through 285 )
5X-RAY DIFFRACTION5chain 'A' and (resid 286 through 336 )
6X-RAY DIFFRACTION6chain 'A' and (resid 337 through 391 )
7X-RAY DIFFRACTION7chain 'A' and (resid 392 through 426 )

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