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- PDB-6vsh: Crystal structure of apo Dicamba Monooxygenase -

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Basic information

Entry
Database: PDB / ID: 6vsh
TitleCrystal structure of apo Dicamba Monooxygenase
ComponentsDicamba O-demethylase, oxygenase component
KeywordsOXIDOREDUCTASE / ELECTRON TRANSPORT
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced iron-sulfur protein as one donor, and incorporation of one atom of oxygen into the other donor / catabolic process / monooxygenase activity / 2 iron, 2 sulfur cluster binding / metal ion binding
Similarity search - Function
Vanillate O-demethylase oxygenase-like, C-terminal catalytic domain / Vanillate O-demethylase oxygenase C-terminal domain / : / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain ...Vanillate O-demethylase oxygenase-like, C-terminal catalytic domain / Vanillate O-demethylase oxygenase C-terminal domain / : / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Dicamba O-demethylase, oxygenase component
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsRydel, T.J.
CitationJournal: J. Mol. Biol. / Year: 2009
Title: Dicamba monooxygenase: structural insights into a dynamic Rieske oxygenase that catalyzes an exocyclic monooxygenation.
Authors: D'Ordine, R.L. / Rydel, T.J. / Storek, M.J. / Sturman, E.J. / Moshiri, F. / Bartlett, R.K. / Brown, G.R. / Eilers, R.J. / Dart, C. / Qi, Y. / Flasinski, S. / Franklin, S.
History
DepositionFeb 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dicamba O-demethylase, oxygenase component
B: Dicamba O-demethylase, oxygenase component
C: Dicamba O-demethylase, oxygenase component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,4536
Polymers115,9253
Non-polymers5273
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-87 kcal/mol
Surface area42800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.170, 80.170, 159.346
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAMETMET(chain 'A' and (resid 2 through 158 or resid 180 through 342 or resid 501))AA2 - 1562 - 156
12GLUGLUARGARG(chain 'A' and (resid 2 through 158 or resid 180 through 342 or resid 501))AA180 - 341180 - 341
13FESFESFESFES(chain 'A' and (resid 2 through 158 or resid 180 through 342 or resid 501))AD501
24ALAALAMETMET(chain 'B' and (resid 2 through 177 or resid 180 through 342 or resid 501))BB2 - 1562 - 156
25GLUGLUARGARG(chain 'B' and (resid 2 through 177 or resid 180 through 342 or resid 501))BB180 - 341180 - 341
26FESFESFESFES(chain 'B' and (resid 2 through 177 or resid 180 through 342 or resid 501))BE501
37ALAALAMETMETchain 'C'CC2 - 1562 - 156
38GLUGLUARGARGchain 'C'CC180 - 341180 - 341
39FESFESFESFESchain 'C'CF501

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Components

#1: Protein Dicamba O-demethylase, oxygenase component / Dicamba monooxygenase / DMO / Three-component Rieske non-heme iron oxygenase system


Mass: 38641.695 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Gene: ddmC / Plasmid: pET28b(+) / Details (production host): Kanamycin resistant / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5S3I3, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced iron-sulfur protein as one donor, and incorporation of one ...References: UniProt: Q5S3I3, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced iron-sulfur protein as one donor, and incorporation of one atom of oxygen into the other donor
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.6 Å3/Da / Density % sol: 52.7 % / Description: Deep-red, diamond-shaped
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10-20 mg/mL protein in 25 mM Tris-HCl, pH 8.0, 10 mM sodium chloride, 0.1 mM EDTA, trace PMSF + 1:1 reservoir solution (15-20% w/v PEG6000, 100 mM sodium citrate, pH 6.0) in 2-6 uL droplet
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: CCD / Date: Jan 15, 2005 / Details: CuVarimax HR
RadiationMonochromator: Cu Ka / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 45738 / % possible obs: 99.6 % / Redundancy: 8.1 % / Biso Wilson estimate: 52.11 Å2 / Rsym value: 0.075 / Χ2: 0.958 / Net I/σ(I): 25.8
Reflection shellResolution: 3→3.11 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 6.69 / Num. unique obs: 4598 / Rsym value: 0.304 / Χ2: 1.014 / % possible all: 100

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Processing

Software
NameVersionClassification
CNX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GTE

3gte


Resolution: 3→19.26 Å / SU ML: 0.3884 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.082
RfactorNum. reflection% reflection
Rfree0.2517 4055 8.89 %
Rwork0.1926 --
obs0.1979 45620 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 53.2 Å2
Refinement stepCycle: LAST / Resolution: 3→19.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7525 0 12 12 7549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00987720
X-RAY DIFFRACTIONf_angle_d1.277710507
X-RAY DIFFRACTIONf_chiral_restr0.06871146
X-RAY DIFFRACTIONf_plane_restr0.00871397
X-RAY DIFFRACTIONf_dihedral_angle_d7.85531068
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.040.31421420.22731430X-RAY DIFFRACTION99.87
3.04-3.070.31541480.24711502X-RAY DIFFRACTION99.88
3.07-3.110.35141360.25681362X-RAY DIFFRACTION100
3.11-3.150.35751320.2491416X-RAY DIFFRACTION99.87
3.15-3.190.32361400.23391466X-RAY DIFFRACTION100
3.2-3.240.26071400.21811436X-RAY DIFFRACTION100
3.24-3.290.28641400.21281418X-RAY DIFFRACTION99.87
3.29-3.340.28351360.20061444X-RAY DIFFRACTION100
3.34-3.390.27751420.20041424X-RAY DIFFRACTION100
3.39-3.450.29481440.20391435X-RAY DIFFRACTION99.94
3.45-3.510.23761520.20051429X-RAY DIFFRACTION99.94
3.52-3.580.31291280.19981449X-RAY DIFFRACTION99.94
3.58-3.650.29381520.20561476X-RAY DIFFRACTION100
3.66-3.730.28671160.19721388X-RAY DIFFRACTION100
3.73-3.820.2581400.1931474X-RAY DIFFRACTION100
3.82-3.910.23431440.18611406X-RAY DIFFRACTION100
3.92-4.020.26571470.18651458X-RAY DIFFRACTION99.69
4.02-4.140.24261440.18231394X-RAY DIFFRACTION99.87
4.14-4.270.24121400.18261439X-RAY DIFFRACTION99.94
4.27-4.420.19541440.16191456X-RAY DIFFRACTION100
4.42-4.590.22941300.17441392X-RAY DIFFRACTION100
4.59-4.80.25381430.17941453X-RAY DIFFRACTION99.87
4.8-5.050.23791440.20281439X-RAY DIFFRACTION99.81
5.05-5.360.22211240.18771429X-RAY DIFFRACTION99.81
5.36-5.760.28191680.19331437X-RAY DIFFRACTION99.94
5.76-6.320.29081300.20721408X-RAY DIFFRACTION100
6.32-7.20.19531300.2131460X-RAY DIFFRACTION100
7.2-8.890.24681300.1731455X-RAY DIFFRACTION100
8.92-19.260.14871490.1441390X-RAY DIFFRACTION98.28

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