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- PDB-5bkc: Crystal structure of AAD-1 in complex with (R)-diclofop, Mn(II), ... -

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Basic information

Entry
Database: PDB / ID: 5bkc
TitleCrystal structure of AAD-1 in complex with (R)-diclofop, Mn(II), and 2-oxoglutarate
Components(R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase
KeywordsOXIDOREDUCTASE / dioxygenase / herbicide degradation
Function / homology
Function and homology information


(R)-dichlorprop dioxygenase (2-oxoglutarate) / 2-oxoglutarate-dependent dioxygenase activity / L-ascorbic acid binding / metal ion binding / cytoplasm
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 / : / Chem-O0D / (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase
Similarity search - Component
Biological speciesDelftia acidovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChekan, J.R. / Nair, S.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Molecular basis for enantioselective herbicide degradation imparted by aryloxyalkanoate dioxygenases in transgenic plants.
Authors: Chekan, J.R. / Ongpipattanakul, C. / Wright, T.R. / Zhang, B. / Bollinger Jr., J.M. / Rajakovich, L.J. / Krebs, C. / Cicchillo, R.M. / Nair, S.K.
History
DepositionJun 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
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_author.identifier_ORCID
Revision 1.3Sep 27, 2023Group: 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _software.name / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4289
Polymers66,5052
Non-polymers9227
Water12,034668
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-47 kcal/mol
Surface area22810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.764, 97.700, 69.913
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#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: 33252.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Delftia acidovorans (bacteria) / Gene: rdpA / Production host: Escherichia coli (E. coli)
References: UniProt: P83310, (R)-dichlorprop dioxygenase (2-oxoglutarate)

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Non-polymers , 5 types, 675 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-O0D / (2R)-2-{4-[(3,5-dichloropyridin-2-yl)oxy]phenoxy}propanoic acid


Mass: 328.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H11Cl2NO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 668 / 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: 2.2 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 25% PEG 3350 0.3M LiSO4 0.1M Bicine pH 9.0 8 mg/mL AAD-1 Cryo: 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 23, 2014
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.8→85.8 Å / Num. obs: 55192 / % possible obs: 100 % / Redundancy: 9.2 % / CC1/2: 0.999 / Rsym value: 0.111 / Net I/av σ(I): 0.999 / Net I/σ(I): 18.7
Reflection shellResolution: 1.8→1.806 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 541 / CC1/2: 0.801 / Rsym value: 0.929 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GQW

1gqw


Resolution: 1.8→48.85 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.09
RfactorNum. reflection% reflection
Rfree0.201 2740 4.97 %
Rwork0.1625 --
obs0.1644 55138 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4394 0 53 668 5115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074661
X-RAY DIFFRACTIONf_angle_d1.0666375
X-RAY DIFFRACTIONf_dihedral_angle_d13.2291738
X-RAY DIFFRACTIONf_chiral_restr0.047699
X-RAY DIFFRACTIONf_plane_restr0.005839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8310.27951380.22412564X-RAY DIFFRACTION100
1.831-1.86430.24381530.20722563X-RAY DIFFRACTION100
1.8643-1.90020.22751360.18852588X-RAY DIFFRACTION100
1.9002-1.9390.22761310.17672613X-RAY DIFFRACTION100
1.939-1.98110.22431350.17342568X-RAY DIFFRACTION100
1.9811-2.02720.23831190.16872607X-RAY DIFFRACTION100
2.0272-2.07790.24541250.1722615X-RAY DIFFRACTION100
2.0779-2.13410.23991270.16712602X-RAY DIFFRACTION100
2.1341-2.19690.2131320.15852589X-RAY DIFFRACTION100
2.1969-2.26780.21351190.16172641X-RAY DIFFRACTION100
2.2678-2.34890.23071410.15532573X-RAY DIFFRACTION100
2.3489-2.44290.22771400.16222613X-RAY DIFFRACTION100
2.4429-2.55410.20421560.162582X-RAY DIFFRACTION100
2.5541-2.68870.19791460.16152626X-RAY DIFFRACTION100
2.6887-2.85720.19331360.17182603X-RAY DIFFRACTION100
2.8572-3.07780.19791350.16832649X-RAY DIFFRACTION100
3.0778-3.38740.18971490.15642616X-RAY DIFFRACTION100
3.3874-3.87740.17681550.15032660X-RAY DIFFRACTION100
3.8774-4.88440.15861300.13012694X-RAY DIFFRACTION100
4.8844-48.8680.17811370.17512832X-RAY DIFFRACTION100

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