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- PDB-3gl0: Crystal structure of dicamba monooxygenase bound to 3,6 dichloros... -

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Basic information

Entry
Database: PDB / ID: 3gl0
TitleCrystal structure of dicamba monooxygenase bound to 3,6 dichlorosalicylic acid (DCSA)
ComponentsDdmC
KeywordsOXIDOREDUCTASE / Rieske protein / non-heme mononuclear 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
: / FE2/S2 (INORGANIC) CLUSTER / 3,6-dichloro-2-hydroxybenzoic acid / OXYGEN MOLECULE / Dicamba O-demethylase, oxygenase component
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsWilson, M.A. / Dumitru, R. / Jiang, W.Z. / Weeks, D.P.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of dicamba monooxygenase: a Rieske nonheme oxygenase that catalyzes oxidative demethylation.
Authors: Dumitru, R. / Jiang, W.Z. / Weeks, D.P. / Wilson, M.A.
History
DepositionMar 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: 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 / struct_conn / struct_ncs_dom_lim / 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_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 / _struct_ref_seq_dif.details / _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: DdmC
B: DdmC
C: DdmC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,66322
Polymers115,9253
Non-polymers1,73819
Water16,646924
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9420 Å2
ΔGint-89 kcal/mol
Surface area40630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.205, 81.205, 158.557
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 2 - 155 / Label seq-ID: 2 - 155

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein DdmC / dicamba monooxygenase


Mass: 38641.695 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Strain: DI-6 / Gene: ddmC / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5S3I3

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Non-polymers , 6 types, 943 molecules

#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-HXX / 3,6-dichloro-2-hydroxybenzoic acid / 3,6 dichlorosalicylic acid


Mass: 207.011 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H4Cl2O3
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 924 / 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: 52.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 5% PEG 4000, 100 mM sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2007 / Details: Bent Rh coated conical Si mirror
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.75→70 Å / Num. all: 118165 / Num. obs: 117603 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 27.8
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 4 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.6 / Num. unique all: 11814 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXDEphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.75→42.25 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.679 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.1 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20619 5898 5 %RANDOM
Rwork0.1678 ---
obs0.16972 117603 99.5 %-
all-118165 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.13 Å20 Å2
2--0.26 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.75→42.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7672 0 82 924 8678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227925
X-RAY DIFFRACTIONr_bond_other_d00.025377
X-RAY DIFFRACTIONr_angle_refined_deg1.281.9610763
X-RAY DIFFRACTIONr_angle_other_deg0.735313029
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.1895987
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92623.59376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.693151221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8811567
X-RAY DIFFRACTIONr_chiral_restr0.090.21161
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028937
X-RAY DIFFRACTIONr_gen_planes_other00.021608
X-RAY DIFFRACTIONr_nbd_refined0.2270.21608
X-RAY DIFFRACTIONr_nbd_other0.2420.25890
X-RAY DIFFRACTIONr_nbtor_refined0.1870.23782
X-RAY DIFFRACTIONr_nbtor_other0.090.24156
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2643
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2810.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3280.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4370.233
X-RAY DIFFRACTIONr_mcbond_it3.2391.56347
X-RAY DIFFRACTIONr_mcbond_other1.1191.51991
X-RAY DIFFRACTIONr_mcangle_it3.49327926
X-RAY DIFFRACTIONr_scbond_it5.33533446
X-RAY DIFFRACTIONr_scangle_it6.6954.52830
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A886medium positional0.260.5
2B886medium positional0.270.5
3C886medium positional0.250.5
1A1087loose positional0.375
2B1087loose positional0.385
3C1087loose positional0.45
1A886medium thermal1.832
2B886medium thermal1.832
3C886medium thermal1.52
1A1087loose thermal2.4910
2B1087loose thermal2.5110
3C1087loose thermal210
LS refinement shellResolution: 1.75→1.794 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 449 -
Rwork0.257 8298 -
obs--99.61 %

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