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- PDB-3rmk: Toluene 4 monooxygenase H with 4-bromophenol -

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Basic information

Entry
Database: PDB / ID: 3rmk
TitleToluene 4 monooxygenase H with 4-bromophenol
Components(Toluene-4-monooxygenase system protein ...) x 3
KeywordsOXIDOREDUCTASE / Aromatic Hydrocarbon Catabolism / Iron / Multi-Component Monooxygenase / Diiron
Function / homology
Function and homology information


toluene 4-monooxygenase / toluene catabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / monooxygenase activity / metal ion binding
Similarity search - Function
TmoB-like / Toluene-4-monooxygenase system B / TmoB-like superfamily / Toluene-4-monooxygenase system protein B (TmoB) / Methane/phenol monooxygenase, hydroxylase component / Propane/methane/phenol/toluene hydroxylase / Methane/Phenol/Alkene Hydroxylase / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase-like ...TmoB-like / Toluene-4-monooxygenase system B / TmoB-like superfamily / Toluene-4-monooxygenase system protein B (TmoB) / Methane/phenol monooxygenase, hydroxylase component / Propane/methane/phenol/toluene hydroxylase / Methane/Phenol/Alkene Hydroxylase / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase-like / Ferritin-like superfamily / Ubiquitin-like (UB roll) / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
4-BROMOPHENOL / : / TRIETHYLENE GLYCOL / Toluene-4-monooxygenase system, hydroxylase component subunit alpha / Toluene-4-monooxygenase system, hydroxylase component subunit gamma / Toluene-4-monooxygenase system, hydroxylase component subunit beta
Similarity search - Component
Biological speciesPseudomonas mendocina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsBailey, L.J. / McCoy, J.G. / Phillips Jr., G.N. / Fox, B.G.
CitationJournal: Biochemistry / Year: 2012
Title: Crystallographic analysis of active site contributions to regiospecificity in the diiron enzyme toluene 4-monooxygenase.
Authors: Bailey, L.J. / Acheson, J.F. / McCoy, J.G. / Elsen, N.L. / Phillips Jr., G.N. / Fox, B.G.
History
DepositionApr 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references
Revision 1.2Jan 30, 2013Group: Database references / Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 A
B: Toluene-4-monooxygenase system protein E
C: Toluene-4-monooxygenase system protein B
D: Toluene-4-monooxygenase system protein A
E: Toluene-4-monooxygenase system protein E
F: Toluene-4-monooxygenase system protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,39737
Polymers205,6756
Non-polymers2,72231
Water28,1931565
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Toluene-4-monooxygenase system protein A
E: Toluene-4-monooxygenase system protein E
F: Toluene-4-monooxygenase system protein B
hetero molecules

A: Toluene-4-monooxygenase system protein A
B: Toluene-4-monooxygenase system protein E
C: Toluene-4-monooxygenase system protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,39737
Polymers205,6756
Non-polymers2,72231
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area30190 Å2
ΔGint-288 kcal/mol
Surface area58720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.544, 176.771, 56.068
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-1-

CA

21E-1338-

HOH

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Components

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Toluene-4-monooxygenase system protein ... , 3 types, 6 molecules ADBECF

#1: Protein Toluene-4-monooxygenase system protein A


Mass: 57322.230 Da / Num. of mol.: 2 / Fragment: Residues 2-493
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Strain: KR1 / Gene: tmoA / Plasmid: p58kABE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q00456, 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: Protein Toluene-4-monooxygenase system protein E


Mass: 36045.449 Da / Num. of mol.: 2 / Fragment: Residues 2-307
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Strain: KR1 / Gene: tmoE / Plasmid: p58kABE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q00460, 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
#3: Protein Toluene-4-monooxygenase system protein B


Mass: 9469.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Strain: KR1 / Gene: tmoB / Plasmid: p58kABE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q00457, 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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Non-polymers , 5 types, 1596 molecules

#4: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#5: Chemical
ChemComp-BML / 4-BROMOPHENOL / Bromophenol


Mass: 173.007 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H5BrO
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1565 / 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: 2.04 Å3/Da / Density % sol: 39.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Protein Solution (0.1 Calcium Chloride, 15% MePEG 2K, 10 mM 4-bromophenol, 0.1 M Hepes, pH 7.5), vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 7, 2010 / Details: mirrors and beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.95→43 Å / Num. all: 123902 / Num. obs: 123099 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→43 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.14 / SU B: 3.15 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1964 6175 5 %RANDOM
Rwork0.1573 ---
obs0.1593 123099 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 138.93 Å2 / Biso mean: 15.2345 Å2 / Biso min: 2.83 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.95→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14432 0 112 1565 16109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02115049
X-RAY DIFFRACTIONr_angle_refined_deg1.021.93120446
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.14151783
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08523.865784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.281152473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.79315100
X-RAY DIFFRACTIONr_chiral_restr0.0750.22074
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111804
X-RAY DIFFRACTIONr_mcbond_it0.5031.58834
X-RAY DIFFRACTIONr_mcangle_it0.98214243
X-RAY DIFFRACTIONr_scbond_it1.63636215
X-RAY DIFFRACTIONr_scangle_it2.6724.56189
LS refinement shellResolution: 1.95→1.999 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 443 -
Rwork0.223 8185 -
all-8628 -
obs--95.68 %

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