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- PDB-5tdu: Toluene 4-monooxygenase (T4moHD) bound to product after turnover ... -

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Basic information

Entry
Database: PDB / ID: 5tdu
TitleToluene 4-monooxygenase (T4moHD) bound to product after turnover in crystal
Components(Toluene-4-monooxygenase system protein ...) x 4
KeywordsOXIDOREDUCTASE / Diiron
Function / homology
Function and homology information


toluene 4-monooxygenase / toluene 4-monooxygenase activity / toluene catabolic process / monooxygenase activity / metal ion binding
Similarity search - Function
Monooxygenase component MmoB/DmpM / Phenol Hydroxylase P2 Protein / TmoB-like / Toluene-4-monooxygenase system B / TmoB-like superfamily / Toluene-4-monooxygenase system protein B (TmoB) / Monooxygenase component MmoB/DmpM / Monooxygenase component MmoB/DmpM superfamily / MmoB/DmpM family / Methane/phenol monooxygenase, hydroxylase component ...Monooxygenase component MmoB/DmpM / Phenol Hydroxylase P2 Protein / TmoB-like / Toluene-4-monooxygenase system B / TmoB-like superfamily / Toluene-4-monooxygenase system protein B (TmoB) / Monooxygenase component MmoB/DmpM / Monooxygenase component MmoB/DmpM superfamily / MmoB/DmpM family / 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 / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / P-CRESOL / Toluene-4-monooxygenase system, hydroxylase component subunit alpha / Toluene-4-monooxygenase system, hydroxylase component subunit gamma / Toluene-4-monooxygenase system, effector component / Toluene-4-monooxygenase system, hydroxylase component subunit beta
Similarity search - Component
Biological speciesPseudomonas mendocina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.742 Å
AuthorsAcheson, J.F. / Fox, B.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-0843239 United States
Department of Energy (DOE, United States)W-31-109-ENG-38 United States
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 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 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_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.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.value / _struct_conn.pdbx_dist_value / _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

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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
E: Toluene-4-monooxygenase system protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,1937
Polymers114,9734
Non-polymers2203
Water16,250902
1
A: Toluene-4-monooxygenase system protein A
B: Toluene-4-monooxygenase system protein E
C: Toluene-4-monooxygenase system protein B
E: Toluene-4-monooxygenase system protein D
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)230,38614
Polymers229,9478
Non-polymers4406
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Buried area33900 Å2
ΔGint-228 kcal/mol
Surface area62730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.237, 116.003, 180.721
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-918-

HOH

21A-923-

HOH

31B-674-

HOH

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Components

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Toluene-4-monooxygenase system protein ... , 4 types, 4 molecules ABCE

#1: Protein Toluene-4-monooxygenase system protein A / Toluene-4-monooxygenase hydroxylase subunit / T4moH


Mass: 57453.438 Da / Num. of mol.: 1 / 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: 36289.801 Da / Num. of mol.: 1 / Fragment: residues 1-308
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.: 1
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
#4: Protein Toluene-4-monooxygenase system protein D / T4mo effector protein D / T4moD / Toluene-4-monooxygenase effector protein


Mass: 11629.032 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Gene: tmoD / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 RILP
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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Non-polymers , 3 types, 905 molecules

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


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-PCR / P-CRESOL / P-Cresol


Mass: 108.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 902 / 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: 2.26 Å3/Da / Density % sol: 45.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM Bis-Tris ph 6.0, 18% PEG 3350, 200 mM Ammonium Chloride, 10 mM Dithionite, 2 mM Methylviologen

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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: Apr 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98757 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 103656 / % possible obs: 99.4 % / Redundancy: 7.4 % / Net I/σ(I): 27.5
Reflection shellResolution: 1.74→1.77 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.83 / % possible all: 87.5

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Processing

Software
NameVersionClassification
PHENIXdev_1957refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3dhh

3dhh


Resolution: 1.742→47.848 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.16
RfactorNum. reflection% reflection
Rfree0.1798 2000 1.93 %
Rwork0.1395 --
obs0.1403 103656 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.742→47.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8029 0 10 904 8943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068437
X-RAY DIFFRACTIONf_angle_d0.95711494
X-RAY DIFFRACTIONf_dihedral_angle_d13.7963135
X-RAY DIFFRACTIONf_chiral_restr0.0431187
X-RAY DIFFRACTIONf_plane_restr0.0051504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7416-1.78520.26211080.17625462X-RAY DIFFRACTION74
1.7852-1.83340.27291340.16656877X-RAY DIFFRACTION93
1.8334-1.88740.21771430.15147224X-RAY DIFFRACTION97
1.8874-1.94830.211440.14337361X-RAY DIFFRACTION100
1.9483-2.01790.19491460.14547381X-RAY DIFFRACTION100
2.0179-2.09870.1931450.1437404X-RAY DIFFRACTION100
2.0987-2.19430.22621460.13537419X-RAY DIFFRACTION100
2.1943-2.30990.191470.13117409X-RAY DIFFRACTION100
2.3099-2.45470.1741450.137419X-RAY DIFFRACTION100
2.4547-2.64420.17251460.13337455X-RAY DIFFRACTION100
2.6442-2.91020.1721480.14287470X-RAY DIFFRACTION100
2.9102-3.33130.18491470.14867490X-RAY DIFFRACTION100
3.3313-4.19660.1421480.13217541X-RAY DIFFRACTION100
4.1966-47.86590.16841530.13717744X-RAY DIFFRACTION100

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