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- PDB-3gte: Crystal Structure of Dicamba Monooxygenase with Non-heme Iron -

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Basic information

Entry
Database: PDB / ID: 3gte
TitleCrystal Structure of Dicamba Monooxygenase with Non-heme Iron
ComponentsDdmC
KeywordsELECTRON TRANSPORT / OXIDOREDUCTASE / Rieske non-heme iron oxygenase
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
ACETATE ION / : / FE2/S2 (INORGANIC) CLUSTER / Dicamba O-demethylase, oxygenase component
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement WAS PERFORMED USING A PRELIMINARY direct methodO STRUCTURE. THIS EARLY direct methodO 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 A HIGH-REDUNDANCY, 2.29 A WAVELENGTH DATA SET. / Resolution: 1.95 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
DepositionMar 27, 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 13, 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

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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)116,80012
Polymers115,9253
Non-polymers8759
Water9,548530
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8520 Å2
ΔGint-122 kcal/mol
Surface area41900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.110, 81.110, 158.810
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
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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: The purified protein was concentrated to 10-20 mg/ml and buffer exchanged into 25 mM Tris-HCl, pH 8.0, 30-50 mM NaCl, 25 mM sodium citrate. DMO crystals were grown using the vapor diffusion ...Details: The purified protein was concentrated to 10-20 mg/ml and buffer exchanged into 25 mM Tris-HCl, pH 8.0, 30-50 mM NaCl, 25 mM sodium citrate. DMO crystals were grown using the vapor diffusion by sitting drop method, with a reservoir solution of 8-11% PEG 6000, 100 mM sodium acetate buffer pH 5.5, 1 M LiCl, and 4 uL droplets of varying protein-to-precipitant ratios., 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: Jun 29, 2005
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: 1.95→36.12 Å / Num. all: 84535 / Num. obs: 81407 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 31.4
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 2.64 / % possible all: 92

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Processing

Software
NameVersionClassification
SERGUIControl Programdata collection
PHASERphasing
CNXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: molecular replacement WAS PERFORMED USING A PRELIMINARY direct methodO STRUCTURE. THIS EARLY direct methodO STRUCTURE WAS OBTAINED LARGELY USING A HIGH-REDUNDANCY, 1. ...Method to determine structure: molecular replacement WAS PERFORMED USING A PRELIMINARY direct methodO STRUCTURE. THIS EARLY direct methodO 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 A HIGH-REDUNDANCY, 2.29 A WAVELENGTH DATA SET.
Resolution: 1.95→20 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2617 7209 8.5 %random
Rwork0.2349 ---
obs-71130 83.6 %-
Displacement parametersBiso mean: 41.483 Å2
Baniso -1Baniso -2Baniso -3
1--0.125 Å20.3 Å20 Å2
2---0.125 Å20 Å2
3---0.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7855 0 30 530 8415
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
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_it1.2921.5
X-RAY DIFFRACTIONc_mcangle_it2.0712
X-RAY DIFFRACTIONc_scbond_it1.7712
X-RAY DIFFRACTIONc_scangle_it2.5772.5
LS refinement shellResolution: 1.95→2.04 Å
RfactorNum. reflection% reflection
Rfree0.2799 568 10 %
Rwork0.2462 --
obs--83.6 %

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