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

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Basic information

Entry
Database: PDB / ID: 5bkb
TitleCrystal structure of AAD-1 in complex with (R)-dichlorprop, 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 / (2R)-2-(2,4-dichlorophenoxy)propanoic acid / : / DI(HYDROXYETHYL)ETHER / (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase
Similarity search - Component
Biological speciesDelftia acidovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.582 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)67,53711
Polymers66,5052
Non-polymers1,0319
Water13,223734
1
A: (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase
hetero molecules

B: (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,53711
Polymers66,5052
Non-polymers1,0319
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area2910 Å2
ΔGint-56 kcal/mol
Surface area24070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.850, 97.804, 69.881
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 , 6 types, 743 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-FTV / (2R)-2-(2,4-dichlorophenoxy)propanoic acid


Mass: 235.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C9H8Cl2O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 734 / 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: 2.21 Å3/Da / Density % sol: 44.23 %
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-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 21, 2013
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.58→85.9 Å / Num. obs: 80901 / % possible obs: 100 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rsym value: 0.093 / Net I/σ(I): 17.5
Reflection shellResolution: 1.58→1.587 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.956 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 790 / CC1/2: 0.786 / % possible all: 95.8

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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: 1.582→54.196 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.91
RfactorNum. reflection% reflection
Rfree0.1972 3956 4.89 %
Rwork0.1617 --
obs0.1635 80828 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.582→54.196 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4419 0 58 734 5211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114676
X-RAY DIFFRACTIONf_angle_d1.2496389
X-RAY DIFFRACTIONf_dihedral_angle_d13.791740
X-RAY DIFFRACTIONf_chiral_restr0.063701
X-RAY DIFFRACTIONf_plane_restr0.007839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5821-1.60140.25341350.24112695X-RAY DIFFRACTION100
1.6014-1.62170.25721200.21112738X-RAY DIFFRACTION100
1.6217-1.6430.22041300.21112714X-RAY DIFFRACTION100
1.643-1.66550.23261260.19942721X-RAY DIFFRACTION100
1.6655-1.68930.23641400.19962735X-RAY DIFFRACTION100
1.6893-1.71450.24041440.19942706X-RAY DIFFRACTION100
1.7145-1.74130.24121490.18932711X-RAY DIFFRACTION100
1.7413-1.76990.22881510.17942678X-RAY DIFFRACTION100
1.7699-1.80040.241410.17342743X-RAY DIFFRACTION100
1.8004-1.83310.22261280.17552716X-RAY DIFFRACTION100
1.8331-1.86840.23391590.17652706X-RAY DIFFRACTION100
1.8684-1.90650.20491460.16822725X-RAY DIFFRACTION100
1.9065-1.9480.19671430.1692729X-RAY DIFFRACTION100
1.948-1.99330.19331530.15852716X-RAY DIFFRACTION100
1.9933-2.04320.17641550.16252710X-RAY DIFFRACTION100
2.0432-2.09840.20341410.1572725X-RAY DIFFRACTION100
2.0984-2.16020.1931380.15672738X-RAY DIFFRACTION100
2.1602-2.22990.20351510.16032723X-RAY DIFFRACTION100
2.2299-2.30960.2191390.15632762X-RAY DIFFRACTION100
2.3096-2.40210.21571410.15862738X-RAY DIFFRACTION100
2.4021-2.51140.21061240.16222783X-RAY DIFFRACTION100
2.5114-2.64380.18111310.16292757X-RAY DIFFRACTION100
2.6438-2.80940.21461330.16542777X-RAY DIFFRACTION100
2.8094-3.02630.20761430.16872771X-RAY DIFFRACTION100
3.0263-3.33080.1771600.15252767X-RAY DIFFRACTION100
3.3308-3.81270.18651580.14812788X-RAY DIFFRACTION100
3.8127-4.80310.14951450.12632837X-RAY DIFFRACTION100
4.8031-54.22790.18131320.16152963X-RAY DIFFRACTION99

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