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- PDB-2bf2: Crystal structure of native toluene-4-monooxygenase catalytic eff... -

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Basic information

Entry
Database: PDB / ID: 2bf2
TitleCrystal structure of native toluene-4-monooxygenase catalytic effector protein, T4moD
ComponentsTOLUENE-4-MONOOXYGENASE SYSTEM PROTEIN D
KeywordsOXIDOREDUCTASE / CATALYTIC EFFECTOR PROTEIN / MAD PHASING / AROMATIC HYDROCARBON CATABOLISM / MONOOXYGENASE / TOLUENE OXIDATION / FAD / FLAVOPROTEIN / IRON
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsLountos, G.T. / Mitchell, K.H. / Studts, J.M. / Fox, B.G. / Orville, A.M.
Citation
Journal: Biochemistry / Year: 2005
Title: Crystal Structures and Functional Studies of T4Mod, the Toluene 4-Monooxygenase Catalytic Effector Protein
Authors: Lountos, G.T. / Mitchell, K.H. / Studts, J.M. / Fox, B.G. / Orville, A.M.
#1: 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.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization and Preliminary Analysis of Native and N-Terminal Truncated Isoforms of Toluene-4-Monooxygenase Catalytic Effector Protein
Authors: Orville, A.M. / Studts, J.M. / Lountos, G.T. / Mitchell, K.H. / Fox, B.G.
#3: Journal: Protein Expr.Purif / Year: 1999
Title: Application of Fed-Batch Fermentation to the Preparation of Isotopically Labeled or Selenomethionyl-Labeled Proteins
Authors: Studts, J.M. / Fox, B.G.
#4: Journal: Biochemistry / Year: 2002
Title: Combined Participation of Hydroxylase Active Site Residues and Effector Protein Binding in a Para to Ortho Modulation of Toluene-4-Monooxygenase Regiospecificity
Authors: Mitchell, K.H. / Studts, J.M. / Fox, B.G.
#5: 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. / Studts, J.M. / Achim, C. / Kauffmann, K.E. / Munck, E. / Steffan, R.J. / Mcclay, K. / Fox, B.G.
History
DepositionDec 3, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TOLUENE-4-MONOOXYGENASE SYSTEM PROTEIN D
B: TOLUENE-4-MONOOXYGENASE SYSTEM PROTEIN D


Theoretical massNumber of molelcules
Total (without water)22,9962
Polymers22,9962
Non-polymers00
Water1,04558
1
A: TOLUENE-4-MONOOXYGENASE SYSTEM PROTEIN D


Theoretical massNumber of molelcules
Total (without water)11,4981
Polymers11,4981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: TOLUENE-4-MONOOXYGENASE SYSTEM PROTEIN D


Theoretical massNumber of molelcules
Total (without water)11,4981
Polymers11,4981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)86.671, 86.671, 144.325
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 11497.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS MENDOCINA (bacteria) / Strain: KR1 / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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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: 3.5 Å3/Da / Density % sol: 65 %
Crystal growpH: 4.7
Details: PROTEIN CRYSTALLIZED FROM 975MM SODIUM/POTASSIUM PHOSPHATE PH 4.7, 400 MM NACL AND 50 MM SUCCINATE PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.7433
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7433 Å / Relative weight: 1
ReflectionResolution: 2.05→37 Å / Num. obs: 19009 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 6
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.5 / % possible all: 78.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→37 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.095 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1949 10.3 %RANDOM
Rwork0.244 ---
obs0.248 17059 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.23 Å2
Baniso -1Baniso -2Baniso -3
1--2.12 Å2-1.06 Å20 Å2
2---2.12 Å20 Å2
3---3.18 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1579 0 0 58 1637
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211599
X-RAY DIFFRACTIONr_bond_other_d0.0020.021461
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.9612163
X-RAY DIFFRACTIONr_angle_other_deg0.85233397
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2295197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021813
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02305
X-RAY DIFFRACTIONr_nbd_refined0.2070.2332
X-RAY DIFFRACTIONr_nbd_other0.2540.21677
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.21019
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.268
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3560.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3240.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4940.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1361.5991
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.11621597
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6873608
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6844.5566
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.365 118
Rwork0.345 1064

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