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

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Basic information

Entry
Database: PDB / ID: 5bkd
TitleCrystal structure of AAD-1 in complex with (R)-cyhalofop, 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) / L-ascorbic acid binding / 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 / : / Chem-RCF / (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase
Similarity search - Component
Biological speciesDelftia acidovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 / software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)67,70210
Polymers66,5052
Non-polymers1,1978
Water10,377576
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-48 kcal/mol
Surface area22630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.531, 97.421, 69.804
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, 584 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 / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-RCF / (2R)-2-[4-(4-cyano-2-fluorophenoxy)phenoxy]propanoic acid


Mass: 301.269 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H12FNO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 576 / 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: 2.19 Å3/Da / Density % sol: 43.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 25% PEG 3350 0.3 LiSO4 0.1M Bicine pH 9.0 8 mg/mL AAD-1 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.9→85.5 Å / Num. obs: 46644 / % possible obs: 100 % / Redundancy: 8.2 % / CC1/2: 0.998 / Rsym value: 0.119 / Net I/σ(I): 17
Reflection shellResolution: 1.9→1.906 Å / Mean I/σ(I) obs: 2.9 / Num. unique obs: 460 / CC1/2: 0.81 / Rsym value: 0.755 / % possible all: 97.7

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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: 1.9→56.742 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.78
RfactorNum. reflection% reflection
Rfree0.2177 2287 4.91 %
Rwork0.1746 --
obs0.1767 46591 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→56.742 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4419 0 76 576 5071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044702
X-RAY DIFFRACTIONf_angle_d0.8656428
X-RAY DIFFRACTIONf_dihedral_angle_d13.7061755
X-RAY DIFFRACTIONf_chiral_restr0.033703
X-RAY DIFFRACTIONf_plane_restr0.004844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94140.25611320.20682724X-RAY DIFFRACTION100
1.9414-1.98650.26821480.20392729X-RAY DIFFRACTION100
1.9865-2.03620.28861450.20232689X-RAY DIFFRACTION100
2.0362-2.09130.24941280.19622741X-RAY DIFFRACTION100
2.0913-2.15280.21451360.18382732X-RAY DIFFRACTION100
2.1528-2.22230.23551200.18312771X-RAY DIFFRACTION100
2.2223-2.30170.23581550.18082749X-RAY DIFFRACTION100
2.3017-2.39390.21791250.18442743X-RAY DIFFRACTION100
2.3939-2.50280.25031340.18872778X-RAY DIFFRACTION100
2.5028-2.63480.24251620.18482723X-RAY DIFFRACTION100
2.6348-2.79980.2221320.18722796X-RAY DIFFRACTION100
2.7998-3.0160.21151590.1942751X-RAY DIFFRACTION100
3.016-3.31950.18451470.16742785X-RAY DIFFRACTION100
3.3195-3.79970.22091620.16162789X-RAY DIFFRACTION100
3.7997-4.78690.18671610.1352819X-RAY DIFFRACTION100
4.7869-56.76710.19611410.17082985X-RAY DIFFRACTION100

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