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- PDB-2bf5: Crystal structure of a toluene 4-monooxygenase catalytic effector... -

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Basic information

Entry
Database: PDB / ID: 2bf5
TitleCrystal structure of a toluene 4-monooxygenase catalytic effector protein variant missing four N-terminal residues (delta-N4 T4moD)
ComponentsTOLUENE-4-MONOOXYGENASE SYSTEM PROTEIN D
KeywordsOXIDOREDUCTASE / CATALYTIC EFFECTOR PROTEIN / N-TERMINAL TRUNCATED MUTANT / AROMATIC HYDROCARBON CATABOLISM / MONOOXYGENASE / TOLUENE OXIDATION / MOLECULAR REPLACEMENT
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 / MOLECULAR REPLACEMENT / Resolution: 1.71 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: 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.
#2: 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.
#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 1.1Dec 28, 2016Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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

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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)22,2512
Polymers22,2512
Non-polymers00
Water4,288238
1
A: TOLUENE-4-MONOOXYGENASE SYSTEM PROTEIN D


Theoretical massNumber of molelcules
Total (without water)11,1251
Polymers11,1251
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)11,1251
Polymers11,1251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)86.215, 86.215, 86.215
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-2021-

HOH

21A-2022-

HOH

31B-2023-

HOH

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Components

#1: Protein TOLUENE-4-MONOOXYGENASE SYSTEM PROTEIN D / DELTA-N4 TOLUENE 4-MONOOXYGENASE CATALYTIC EFFECTOR


Mass: 11125.419 Da / Num. of mol.: 2 / Fragment: RESIDUES 5-102
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS MENDOCINA (bacteria) / Strain: KR1 / Plasmid: PET3A / 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 / Water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DELTA-N4 T4MOD VARIANT WAS CREATED WITH A VECTOR THAT INITIATES PROTEIN TRANSLATION AT RESIDUE ...THE DELTA-N4 T4MOD VARIANT WAS CREATED WITH A VECTOR THAT INITIATES PROTEIN TRANSLATION AT RESIDUE 5 IN THE OPEN READING FRAME. DETAILS WILL APPEAR IN LOUNTOS ET AL, BIOCHEMISTRY, SUBMITTED.

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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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growDetails: PROTEIN WAS CRYSTALLIZED FROM 2.0 M AMMONIUM SULFATE, 5% (V/V) 2-PROPANOL, AND 1.5% (V/V) 1,2,3-HEPTANETRIOL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0332
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 21, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.71→37 Å / Num. obs: 23407 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 21.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 3.4
Reflection shellResolution: 1.71→1.8 Å / Redundancy: 21.6 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NATIVE TOLUENE 4-MONOOXYGENASE

Resolution: 1.71→37 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.559 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 5-10 IN CHAIN A AND CHAIN B AND RESIDUE 102 IN CHAIN B WERE NOT INCLUDED DUE TO THE LACK OF ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.185 2381 10.2 %RANDOM
Rwork0.154 ---
obs0.157 21007 100 %-
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: 13.37 Å2
Refinement stepCycle: LAST / Resolution: 1.71→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1460 0 0 238 1698
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221492
X-RAY DIFFRACTIONr_bond_other_d0.0020.021380
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.9692015
X-RAY DIFFRACTIONr_angle_other_deg0.89733206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4365181
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_restr0.0960.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021678
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02293
X-RAY DIFFRACTIONr_nbd_refined0.2360.2299
X-RAY DIFFRACTIONr_nbd_other0.260.21661
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.2969
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2167
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3430.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2810.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0461.5912
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.00121475
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2913580
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.6554.5540
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: 1.71→1.75 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.213 191
Rwork0.171 1522

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