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- PDB-4wqm: Structure of the toluene 4-monooxygenase NADH oxidoreductase T4mo... -

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Basic information

Entry
Database: PDB / ID: 4wqm
TitleStructure of the toluene 4-monooxygenase NADH oxidoreductase T4moF, K270S K271S variant
ComponentsToluene-4-monooxygenase electron transfer component
KeywordsOXIDOREDUCTASE / iron-sulfur / ferredoxin-NAD reductase / electron-transfer
Function / homology
Function and homology information


ferredoxin-NAD+ reductase / ferredoxin-NAD+ reductase activity / toluene catabolic process / 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Translation factors / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. ...Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Translation factors / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Elongation Factor Tu (Ef-tu); domain 3 / Flavoprotein pyridine nucleotide cytochrome reductase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Ubiquitin-like (UB roll) / Roll / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / NICKEL (II) ION / Toluene-4-monooxygenase system, ferredoxin--NAD(+) reductase component
Similarity search - Component
Biological speciesPseudomonas mendocina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.62 Å
AuthorsAcheson, J.F. / Fox, B.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-0843239 United States
CitationJournal: Biochemistry / Year: 2015
Title: Structure of T4moF, the Toluene 4-Monooxygenase Ferredoxin Oxidoreductase.
Authors: Acheson, J.F. / Moseson, H. / Fox, B.G.
History
DepositionOct 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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.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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toluene-4-monooxygenase electron transfer component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,71510
Polymers35,8911
Non-polymers1,8249
Water7,566420
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-54 kcal/mol
Surface area15820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.334, 69.074, 68.224
Angle α, β, γ (deg.)90.000, 116.530, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-642-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Toluene-4-monooxygenase electron transfer component


Mass: 35890.855 Da / Num. of mol.: 1 / Mutation: K270S K271S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Gene: tmoF / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / Variant (production host): RILP / References: UniProt: Q03304, ferredoxin-NAD+ reductase

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Non-polymers , 5 types, 429 molecules

#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 16% PEG 3350, 100 mM Bis-Tris, 200 mM Ammonium Acetate, 50 mM Guanidine-HCl, 5 mM NiCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 43392 / % possible obs: 96.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.066 / Χ2: 1.098 / Net I/av σ(I): 18.801 / Net I/σ(I): 11.2 / Num. measured all: 168856
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.62-1.653.70.31720380.71591.3
1.65-1.683.90.27421150.75295.3
1.68-1.713.90.26221340.7895.3
1.71-1.753.90.22521390.82695.9
1.75-1.783.90.19221540.86996.2
1.78-1.823.90.17521520.95296.1
1.82-1.873.90.15121521.09896.3
1.87-1.923.90.13521301.08696.5
1.92-1.983.90.11821771.18796.6
1.98-2.043.90.121691.29296.9
2.04-2.113.90.09221741.39997.1
2.11-2.23.90.08421641.44597
2.2-2.33.90.07621811.28897.4
2.3-2.423.90.07121651.3697.7
2.42-2.573.90.06822201.1997.8
2.57-2.773.90.06421941.29898
2.77-3.053.90.06122151.22898.4
3.05-3.493.90.05722230.95698.6
3.49-4.43.80.04822391.01998.9
4.4-503.70.04322571.15897.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-20002.4.1data collection
PHENIX1.9-1675refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→27.125 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1887 2000 4.61 %
Rwork0.1448 41388 -
obs0.1469 43388 96.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.75 Å2 / Biso mean: 24.9711 Å2 / Biso min: 7.29 Å2
Refinement stepCycle: final / Resolution: 1.62→27.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2515 0 103 420 3038
Biso mean--27.31 34.92 -
Num. residues----326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072733
X-RAY DIFFRACTIONf_angle_d1.1543703
X-RAY DIFFRACTIONf_chiral_restr0.041408
X-RAY DIFFRACTIONf_plane_restr0.004469
X-RAY DIFFRACTIONf_dihedral_angle_d14.7931020
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6154-1.65580.23631330.16482757289090
1.6558-1.70050.21531400.14092897303795
1.7005-1.75060.19631410.12692912305396
1.7506-1.80710.17541420.12762922306496
1.8071-1.87160.20451410.13172944308596
1.8716-1.94660.20731430.14282950309396
1.9466-2.03510.21071430.13942946308997
2.0351-2.14240.21571410.13342943308497
2.1424-2.27650.20011450.13282997314297
2.2765-2.45220.16461430.14492966310998
2.4522-2.69880.2141470.15513016316398
2.6988-3.08880.20861440.15963011315598
3.0888-3.88980.15311480.15193055320399
3.8898-27.12920.17421490.14273072322198

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