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- PDB-6d0o: rdpA dioxygenase holoenzyme -

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Basic information

Entry
Database: PDB / ID: 6d0o
TitlerdpA dioxygenase holoenzyme
Components(R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase
KeywordsOXIDOREDUCTASE / Alpha-ketoglutarate-dependent dioxygenase
Function / homology
Function and homology information


(R)-dichlorprop dioxygenase (2-oxoglutarate) / aromatic compound catabolic process / dioxygenase activity / metal ion binding
Similarity search - Function
Clavaminate synthase-like / Double-stranded beta-helix / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase
Similarity search - Component
Biological speciesSphingobium herbicidovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRydel, T.J. / Sturman, E.J. / Zheng, M. / Evdokimov, A.
CitationJournal: Pest Manag. Sci. / Year: 2019
Title: Development of enzymes for robust aryloxyphenoxypropionate and synthetic auxin herbicide tolerance traits in maize and soybean crops.
Authors: Larue, C.T. / Goley, M. / Shi, L. / Evdokimov, A.G. / Sparks, O.C. / Ellis, C. / Wollacott, A.M. / Rydel, T.J. / Halls, C.E. / Van Scoyoc, B. / Fu, X. / Nageotte, J.R. / Adio, A.M. / Zheng, ...Authors: Larue, C.T. / Goley, M. / Shi, L. / Evdokimov, A.G. / Sparks, O.C. / Ellis, C. / Wollacott, A.M. / Rydel, T.J. / Halls, C.E. / Van Scoyoc, B. / Fu, X. / Nageotte, J.R. / Adio, A.M. / Zheng, M. / Sturman, E.J. / Garvey, G.S. / Varagona, M.J.
History
DepositionApr 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Mar 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ncs_dom_lim
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase
B: (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase
C: (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase
D: (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,72912
Polymers135,9094
Non-polymers8208
Water9,998555
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8790 Å2
ΔGint-84 kcal/mol
Surface area45680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.014, 153.014, 156.845
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGAA11 - 29611 - 296
21ARGARGBB11 - 29611 - 296
12PHEPHEAA12 - 29812 - 298
22PHEPHECC12 - 29812 - 298
13ARGARGAA11 - 29911 - 299
23ARGARGDD11 - 29911 - 299
14PHEPHEBB12 - 29712 - 297
24PHEPHECC12 - 29712 - 297
15ARGARGBB11 - 29711 - 297
25ARGARGDD11 - 29711 - 297
16PHEPHECC12 - 29712 - 297
26PHEPHEDD12 - 29712 - 297

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
(R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase / RdpA / (R)-dichlorprop/(R)-mecoprop dioxygenase / Alpha-ketoglutarate-dependent dioxygenase / ...RdpA / (R)-dichlorprop/(R)-mecoprop dioxygenase / Alpha-ketoglutarate-dependent dioxygenase / Dichlorprop/alpha-ketoglutarate-dioxygenase / Mecoprop/alpha-ketoglutarate-dioxygenase


Mass: 33977.246 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium herbicidovorans (strain ATCC 700291 / DSM 11019 / NBRC 16415 / MH) (bacteria)
Strain: ATCC 700291 / DSM 11019 / NBRC 16415 / MH / Gene: rdpA / Production host: Escherichia coli (E. coli)
References: UniProt: Q8KSC8, (R)-dichlorprop dioxygenase (2-oxoglutarate)
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 3.45 Å3/Da / Density % sol: 64.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: The protein solution was 10-20 mg/ml in 20mM Tris-pH 8, 50mM NaCl, 5mM bME. The precipitant solution was 0.1M Hepes-pH 7.5, 10(w/v)% PEG 8K, 8(v/v)% ethylene glycol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→109.6 Å / Num. obs: 79857 / % possible obs: 100 % / Redundancy: 6.9 % / Rsym value: 0.113 / Net I/σ(I): 23.5
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 6.7 % / Num. unique obs: 3967 / Rsym value: 0.761 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.229 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.189 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22843 3793 4.8 %RANDOM
Rwork0.18586 ---
obs0.18782 76047 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.479 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å2-0 Å2-0 Å2
2--0.39 Å2-0 Å2
3----0.79 Å2
Refinement stepCycle: 1 / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8891 0 44 555 9490
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0199178
X-RAY DIFFRACTIONr_bond_other_d0.0020.028213
X-RAY DIFFRACTIONr_angle_refined_deg1.9751.93412491
X-RAY DIFFRACTIONr_angle_other_deg1.212318995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.74751113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89223.085457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.328151435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6821578
X-RAY DIFFRACTIONr_chiral_restr0.1720.21358
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02110320
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021970
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.814.3474467
X-RAY DIFFRACTIONr_mcbond_other4.7794.3454466
X-RAY DIFFRACTIONr_mcangle_it7.0216.4815572
X-RAY DIFFRACTIONr_mcangle_other7.0236.4845573
X-RAY DIFFRACTIONr_scbond_it5.2654.8764711
X-RAY DIFFRACTIONr_scbond_other5.2244.8754707
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.657.1116915
X-RAY DIFFRACTIONr_long_range_B_refined10.33149.72510043
X-RAY DIFFRACTIONr_long_range_B_other10.32549.6249970
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A168780.09
12B168780.09
21A166400.1
22C166400.1
31A167380.11
32D167380.11
41B163620.11
42C163620.11
51B166520.1
52D166520.1
61C182600.08
62D182600.08
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 310 -
Rwork0.246 5501 -
obs--98.73 %

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