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- PDB-5tds: Toluene bound in the resting active site of toluene 4-monooxygena... -

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Basic information

Entry
Database: PDB / ID: 5tds
TitleToluene bound in the resting active site of toluene 4-monooxygenase (T4moH)
Components(Toluene-4-monooxygenase system protein ...) x 3
KeywordsOXIDOREDUCTASE / Diiron / hydroxylase / substrate complex
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
: / TOLUENE / 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 / Resolution: 1.719 Å
AuthorsAcheson, J.F. / Fox, B.G.
CitationJournal: Nature / Year: 2017
Title: In-crystal reaction cycle of a toluene-bound diiron hydroxylase.
Authors: Acheson, J.F. / Bailey, L.J. / Brunold, T.C. / Fox, B.G.
History
DepositionSep 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Apr 26, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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.ptnr1_symmetry / _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.ptnr2_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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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)212,28229
Polymers210,9756
Non-polymers1,30723
Water35,9041993
1
A: Toluene-4-monooxygenase system protein A
B: Toluene-4-monooxygenase system protein E
C: Toluene-4-monooxygenase system protein B
hetero molecules

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)212,28229
Polymers210,9756
Non-polymers1,30723
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area28900 Å2
ΔGint-223 kcal/mol
Surface area57810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.386, 176.906, 55.944
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-847-

HOH

21B-886-

HOH

31E-745-

HOH

41E-779-

HOH

51E-799-

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 / Toluene-4-monooxygenase hydroxylase subunit / T4moH


Mass: 57453.438 Da / Num. of mol.: 2 / Fragment: residues 1-493
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Gene: tmoA / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 RILP
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 / T4moE


Mass: 38433.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Gene: tmoE / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 RILP
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 / T4moB


Mass: 9600.989 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Gene: tmoB / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 RILP
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, 2016 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-MBN / TOLUENE / Toluene


Mass: 92.138 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C7H8
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1993 / 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: 1.99 Å3/Da / Density % sol: 38.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM MOPS/HEPES pH 7.5, 100 mM MgCl2, 10% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.98757 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 11, 2011
RadiationMonochromator: C111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98757 Å / Relative weight: 1
ReflectionResolution: 1.719→50 Å / Num. obs: 177282 / % possible obs: 99.1 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 3.22
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 5.1 % / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3dhg

3dhg


Resolution: 1.719→40.782 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.96
RfactorNum. reflection% reflection
Rfree0.1731 2009 1.13 %
Rwork0.1301 --
obs0.1305 177282 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.719→40.782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14392 0 77 1993 16462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00615025
X-RAY DIFFRACTIONf_angle_d0.98320411
X-RAY DIFFRACTIONf_dihedral_angle_d13.3845474
X-RAY DIFFRACTIONf_chiral_restr0.042066
X-RAY DIFFRACTIONf_plane_restr0.0052653
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7186-1.76160.20781370.137811769X-RAY DIFFRACTION94
1.7616-1.80920.22881370.127912375X-RAY DIFFRACTION98
1.8092-1.86250.19231550.124112394X-RAY DIFFRACTION99
1.8625-1.92260.20461380.123912377X-RAY DIFFRACTION99
1.9226-1.99130.19761410.127712427X-RAY DIFFRACTION99
1.9913-2.0710.17051420.120712396X-RAY DIFFRACTION99
2.071-2.16530.18121330.117712411X-RAY DIFFRACTION99
2.1653-2.27940.16861480.116912457X-RAY DIFFRACTION99
2.2794-2.42220.17151450.122312517X-RAY DIFFRACTION99
2.4222-2.60920.17181420.13112576X-RAY DIFFRACTION99
2.6092-2.87170.18531440.139612675X-RAY DIFFRACTION100
2.8717-3.28710.15891520.141512772X-RAY DIFFRACTION100
3.2871-4.14080.16141400.124412859X-RAY DIFFRACTION100
4.1408-40.79350.15331550.140813268X-RAY DIFFRACTION100

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