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- PDB-3gb4: Crystal Structure of Dicamba Monooxygenase with Non-heme Cobalt a... -

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Basic information

Entry
Database: PDB / ID: 3gb4
TitleCrystal Structure of Dicamba Monooxygenase with Non-heme Cobalt and Dicamba
ComponentsDdmC
KeywordsELECTRON TRANSPORT / OXIDOREDUCTASE / Rieske non-heme iron oxygenase / 2Fe-2S / Iron / Iron-sulfur / Metal-binding
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 / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / 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
: / 3,6-dichloro-2-methoxybenzoic acid / FE2/S2 (INORGANIC) CLUSTER / Dicamba O-demethylase, oxygenase component
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsRydel, T.J. / Sturman, E.J. / Moshiri, F. / Brown, G.R. / Qi, Y.
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.J.
History
DepositionFeb 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
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_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DdmC
B: DdmC
C: DdmC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,30715
Polymers115,9253
Non-polymers1,38212
Water9,386521
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8350 Å2
ΔGint-152 kcal/mol
Surface area43140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.550, 81.550, 161.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein DdmC


Mass: 38641.695 Da / Num. of mol.: 3 / Mutation: M1A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Gene: ddmC / Plasmid: pET28b(+) kanamycin resistant / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5S3I3
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-D3M / 3,6-dichloro-2-methoxybenzoic acid / Dicamba


Mass: 221.037 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H6Cl2O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / 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: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Equal volumes of protein (10-20 mg/mL in 30 mM Tri-HCl,pH 8.0, 0.1 mM EDTA, with trace PMSF) and precipitant solution (15-20%(w/v) PEG 6000 and 0.1 M sodium citrate pH 6.0) were used to make ...Details: Equal volumes of protein (10-20 mg/mL in 30 mM Tri-HCl,pH 8.0, 0.1 mM EDTA, with trace PMSF) and precipitant solution (15-20%(w/v) PEG 6000 and 0.1 M sodium citrate pH 6.0) were used to make the sitting drop. The data collection crystal was transferred to a cryo-amenable soak solution containing 24% PEG 6000, 24% glycerol, 0.1M HEPES-pH 7, 10 mM CoCl2, and 1.25 mM dicamba for 24 hours prior to being plunge-cooled in liquid nitrogen for data collection, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 11, 2006
RadiationMonochromator: Rosenbaum-Rock monochromator with high-resolution double-crystal Si(220) sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 74823 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 23.1
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 1.66 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SERGUIControl Programdata collection
PHASERphasing
CNXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MR was performed using a preliminary DMO structure. This early DMO structure was obtained largely using a high-redundancy, 1.5418 A wavelength data set for Fe single anomalous ...Starting model: MR was performed using a preliminary DMO structure. This early DMO structure was obtained largely using a high-redundancy, 1.5418 A wavelength data set for Fe single anomalous dispersion (SAD) phasing, with assistance from the sulfur anomalous signal in the 2.29 A wavelength data set.

Resolution: 2.05→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 6177 8.2 %random
Rwork0.221 ---
all0.243 75230 --
obs0.225 61905 82.3 %-
Displacement parametersBiso mean: 45.466 Å2
Baniso -1Baniso -2Baniso -3
1--0.026 Å2-0.126 Å20 Å2
2---0.026 Å20 Å2
3---0.052 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7926 0 45 521 8492
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_deg1.32
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.3641.5
X-RAY DIFFRACTIONc_mcangle_it2.2312
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it2.9372.5
LS refinement shellResolution: 2.05→2.14 Å
RfactorNum. reflection% reflection
Rfree0.245 469 -
Rwork0.209 --
obs--82 %

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