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- PDB-2ind: Mn(II) Reconstituted Toluene/o-xylene Monooxygenase Hydroxylase X... -

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Basic information

Entry
Database: PDB / ID: 2ind
TitleMn(II) Reconstituted Toluene/o-xylene Monooxygenase Hydroxylase X-ray Crystal Structure
Components
  • (Toluene, o-xylene monooxygenase oxygenase ...) x 2
  • TouB protein
KeywordsOXIDOREDUCTASE / manganese reconstitution / 4-helix bundle / carboxylate bridge / metalloenzyme
Function / homology
Function and homology information


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
YHS domain / YHS domain / 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 ...YHS domain / YHS domain / 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 o-xylene monooxygenase oxygenase subunit TouA / Toluene o-xylene monooxygenase component TouB / Toluene o-xylene monooxygenase component TouE
Similarity search - Component
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMcCormick, M.S. / Sazinsky, M.H. / Condon, K.L. / Lippard, S.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2006
Title: X-ray crystal structures of manganese(II)-reconstituted and native toluene/o-xylene monooxygenase hydroxylase reveal rotamer shifts in conserved residues and an enhanced view of the protein interior.
Authors: McCormick, M.S. / Sazinsky, M.H. / Condon, K.L. / Lippard, S.J.
History
DepositionOct 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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 / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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_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, o-xylene monooxygenase oxygenase subunit
B: Toluene, o-xylene monooxygenase oxygenase subunit
C: TouB protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6536
Polymers104,2613
Non-polymers3923
Water2,540141
1
A: Toluene, o-xylene monooxygenase oxygenase subunit
B: Toluene, o-xylene monooxygenase oxygenase subunit
C: TouB protein
hetero molecules

A: Toluene, o-xylene monooxygenase oxygenase subunit
B: Toluene, o-xylene monooxygenase oxygenase subunit
C: TouB protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,30612
Polymers208,5226
Non-polymers7846
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_553-x,-x+y,-z-5/31
Unit cell
Length a, b, c (Å)182.521, 182.521, 67.792
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe second half of the dimeric biological assembly is generated by the two fold axis: -x, -x+y, (-z+1/3)-5/3

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Components

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Toluene, o-xylene monooxygenase oxygenase ... , 2 types, 2 molecules AB

#1: Protein Toluene, o-xylene monooxygenase oxygenase subunit


Mass: 57039.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Strain: OX1 / Gene: touA / Plasmid: PET22B(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O87798
#2: Protein Toluene, o-xylene monooxygenase oxygenase subunit / Toluene o-xylene monooxygenase component


Mass: 37551.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Strain: OX1 / Gene: touE / Plasmid: PET22B(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O87802

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Protein , 1 types, 1 molecules C

#3: Protein TouB protein / Toluene o-xylene monooxygenase component


Mass: 9670.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Strain: OX1 / Gene: touB / Plasmid: PET22B(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O87799

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Non-polymers , 3 types, 144 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 3.13 Å3/Da / Density % sol: 60.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 2.1-2.5 M ammonium sulfate, 2-4% PEG 400, 10-20 mM manganese chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 2, 2004
Details: Flat collimating mirror, double crystal monochromator, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 64565 / Num. obs: 64565 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rsym value: 0.069 / Χ2: 1.304 / Net I/σ(I): 17.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 4.5 / Num. unique all: 6028 / Rsym value: 0.431 / Χ2: 1.366 / % possible all: 91.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
Blu-Icedata collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1T0Q

1t0q


Resolution: 2.2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2972 4.5 %RANDOM
Rwork0.217 ---
all0.217 58566 --
obs0.217 58566 89 %-
Solvent computationBsol: 40.012 Å2
Displacement parametersBiso mean: 50.745 Å2
Baniso -1Baniso -2Baniso -3
1-17.747 Å24.608 Å20 Å2
2--17.747 Å20 Å2
3----35.494 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7346 0 21 141 7508
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.256
X-RAY DIFFRACTIONc_mcbond_it1.2371.5
X-RAY DIFFRACTIONc_scbond_it1.9342
X-RAY DIFFRACTIONc_mcangle_it1.9992
X-RAY DIFFRACTIONc_scangle_it2.7972.5
LS refinement shellResolution: 2.2→2.28 Å /
RfactorNum. reflection
Rwork0.431 -
obs-6028
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5p6g_xplor_par.txtp6g_xplor_top.txt

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