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- PDB-1g11: TOLUENE-4-MONOOXYGENASE CATALYTIC EFFECTOR PROTEIN NMR STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1g11
TitleTOLUENE-4-MONOOXYGENASE CATALYTIC EFFECTOR PROTEIN NMR STRUCTURE
ComponentsTOLUENE-4-MONOOXYGENASE CATALYTIC EFFECTOR
KeywordsOXIDOREDUCTASE / aromatic hydrocarbon catabolism / monooxygenase / toluene oxidation
Function / homology
Function and homology information


toluene catabolic process / monooxygenase activity
Similarity search - Function
Monooxygenase component MmoB/DmpM / Phenol Hydroxylase P2 Protein / Monooxygenase component MmoB/DmpM / Monooxygenase component MmoB/DmpM superfamily / MmoB/DmpM family / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Toluene-4-monooxygenase system, effector component
Similarity search - Component
Biological speciesPseudomonas mendocina (bacteria)
MethodSOLUTION NMR / DISTANCE GEOMETRY SIMULATED ANNEALING, TORSION ANGLE MOLECULAR DYNAMICS
AuthorsHemmi, H. / Studts, J.M. / Chae, Y.K. / Song, J. / Markley, J.L. / Fox, B.G.
Citation
Journal: Biochemistry / Year: 2001
Title: Solution structure of the toluene 4-monooxygenase effector protein (T4moD).
Authors: Hemmi, H. / Studts, J.M. / Chae, Y.K. / Song, J. / Markley, J.L. / Fox, B.G.
#1: Journal: J.BIOMOL.NMR / Year: 2000
Title: Assignment of 1H, 13C and 15N NMR Signals in the Toluene 4-monooxygenase Effector Protein
Authors: Hemmi, H. / Studts, J.M. / Chae, Y.K. / Fox, B.G. / Markley, J.L.
#2: Journal: PROTEIN EXPR.PURIF. / Year: 1999
Title: Application of Fed-batch Fermentation to the Preparation of Isotopicaly Labeled or Selenomethionyl-labeled Proteins
Authors: Studts, J.M. / Fox, B.G.
#3: Journal: Biochemistry / Year: 1999
Title: Detection and Classification of Hyperfine-shifted 1H, 2H, and 15N Resonances of the Rieske Ferredoxin Component from Toluene 4-monooxygenase
Authors: Xia, B. / Pikus, J.D. / Xia, W. / McClay, K. / Steffan, R.J. / Chae, Y.K. / Westler, M.M. / Markley, J.L. / Fox, B.G.
#4: Journal: Biochemistry / Year: 1996
Title: Recombinant Toluene-4-monooxygenase: Catalytic and Mossbauer Studies of the Purified Diiron and Rieske Components of a Four-Protein Complex
Authors: Pikus, J.D. / M Studts, J. / Achim, C. / Kauffmann, K.E. / Munck, E. / Steffan, R.J. / Mcclay, K. / Fox, B.G.
#5: Journal: J.BACTERIOL. / Year: 1991
Title: Toluene-4-monooxygenase, a Three Component Enzyme System that Catalyzes the Oxidation of Toluene to p-Cresol in Pseudomonas mendocina KR1
Authors: Whited, G.M. / Gibson, D.T.
History
DepositionOct 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TOLUENE-4-MONOOXYGENASE CATALYTIC EFFECTOR


Theoretical massNumber of molelcules
Total (without water)11,4981
Polymers11,4981
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 60target function
RepresentativeModel #1one of ensemble

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Components

#1: Protein TOLUENE-4-MONOOXYGENASE CATALYTIC EFFECTOR / TOLUENE-4-MONOOXYGENASE SYSTEM PROTEIN D / T4MOD


Mass: 11497.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Strain: KR1 / Plasmid: PET15B / Production host: Escherichia coli (E. coli)
References: UniProt: Q00459, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 1H-15N HSQC,HNCA,HN(CO)CA,C(CO)NH,HN(CA)CB,(H)CCH-COSY,(H)CCH-TOCSY,2D 1H-NOESY,2D 1H-TOCSY,CT-13C-HSQC,3D NOESY-CT-HSCQ,3D TOCSY-CT-HSQC
NMR detailsText: 123 1H-15N CROSS PEAKS WERE ASSIGNED OUT OF THE EXPECTED 129 CROSS PEAKS (95% COMPLETE). 386 BACKBONE RESONANCES WERE ASSIGNED OUT OF THE EXPECTED 400 RESONANCES (97% COMPLETE). 789 SIDECHAIN ...Text: 123 1H-15N CROSS PEAKS WERE ASSIGNED OUT OF THE EXPECTED 129 CROSS PEAKS (95% COMPLETE). 386 BACKBONE RESONANCES WERE ASSIGNED OUT OF THE EXPECTED 400 RESONANCES (97% COMPLETE). 789 SIDECHAIN RESONANCES WERE ASSIGNED OUT OF THE EXPECTED 901 RESONANCES (88% COMPLETE). ARG SIDECHAIN ATOMS ACCOUNT FOR 51 OF 112 UNASSIGNED SIDECHAIN ATOMS (51%).

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM [U-13C,U-15N] T4moD50 mM phosphate pH 7.0, 90% H20/10% D20 or 99.9% D20, 0.5 uM azide, protease inhibitor cocktail product no. p 27124, Sigma Chemical Co, St. Louis, MO
23.0 mM [NA] T4moD50 mM phosphate pH 7.0, 90% H20/10% D20 or 99.9% D20, 0.5 uM azide, protease inhibitor cocktail product no. p 27124, Sigma Chemical Co, St. Louis, MO
Sample conditionsIonic strength: 67 mM / pH: 7 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.843BRUNGERstructure solution
DYANA1.5GUNTER, MUMENTHALER, WUTRICHrefinement
RefinementMethod: DISTANCE GEOMETRY SIMULATED ANNEALING, TORSION ANGLE MOLECULAR DYNAMICS
Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON 1339 interproton restraints. These comprised 367 intraresidue, 424 sequential, 195 medium-range, and 273 long-range NOE distance restraints and 128 dihedral angle ...Details: THE STRUCTURES ARE BASED ON 1339 interproton restraints. These comprised 367 intraresidue, 424 sequential, 195 medium-range, and 273 long-range NOE distance restraints and 128 dihedral angle restraints (78 psi, 26 phi, and 24 chi), AND 80 HYDROGEN BONDING reSTRAINTS.
NMR representativeSelection criteria: one of ensemble
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 60 / Conformers submitted total number: 20

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