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- PDB-6d3j: FT_T dioxygenase holoenzyme -

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Basic information

Entry
Database: PDB / ID: 6d3j
TitleFT_T dioxygenase holoenzyme
ComponentsFT_T dioxygenase
KeywordsOXIDOREDUCTASE / Alpha-ketoglutarate-dependent dioxygenase
Function / homology
Function and homology information


(R)-dichlorprop dioxygenase (2-oxoglutarate) / 2-oxoglutarate-dependent dioxygenase activity / catabolic process / 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 / : / (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase
Similarity search - Component
Biological speciesSphingobium herbicidovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsRydel, T.J. / Halls, C.E.
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 16, 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: 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_struct_conn_angle / refine_hist / 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 / _refine_hist.d_res_low / _struct_conn.pdbx_dist_value / _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: FT_T dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,30014
Polymers33,4471
Non-polymers85313
Water181
1
A: FT_T dioxygenase
hetero molecules

A: FT_T dioxygenase
hetero molecules

A: FT_T dioxygenase
hetero molecules

A: FT_T dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,20056
Polymers133,7874
Non-polymers3,41352
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
crystal symmetry operation12_545x,x-y-1,-z+1/31
Buried area12330 Å2
ΔGint-307 kcal/mol
Surface area41270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.413, 137.413, 76.261
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein FT_T dioxygenase


Mass: 33446.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: engineered variant / Source: (gene. exp.) Sphingobium herbicidovorans (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KSC8*PLUS
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.11 Å3/Da / Density % sol: 60.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: precipitant solution: 2.5 M NaCl, 0.1M KP04/NaP04-pH 6.2; protein solution: 10-20 mg/ml in 30 mM Tris-8, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→119 Å / Num. obs: 8906 / % possible obs: 99.9 % / Redundancy: 20 % / Rsym value: 0.104 / Net I/σ(I): 39.5
Reflection shellResolution: 3→3.05 Å / Rsym value: 0.498 / % 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: 3→119 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.888 / SU B: 35.813 / SU ML: 0.296 / Cross valid method: THROUGHOUT / ESU R: 1.198 / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2742 423 4.7 %RANDOM
Rwork0.1945 ---
obs0.1982 8483 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 90.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å2-0.37 Å2-0 Å2
2---0.75 Å20 Å2
3---2.42 Å2
Refinement stepCycle: 1 / Resolution: 3→119 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1975 0 22 1 1998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192036
X-RAY DIFFRACTIONr_bond_other_d0.0020.021840
X-RAY DIFFRACTIONr_angle_refined_deg2.2211.9462772
X-RAY DIFFRACTIONr_angle_other_deg1.25134260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2755244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14823.43896
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.55115322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2071514
X-RAY DIFFRACTIONr_chiral_restr0.1240.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212256
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02430
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_it3.4755.569985
X-RAY DIFFRACTIONr_mcbond_other3.4755.57984
X-RAY DIFFRACTIONr_mcangle_it5.4728.3411226
X-RAY DIFFRACTIONr_mcangle_other5.478.341227
X-RAY DIFFRACTIONr_scbond_it3.6865.9411051
X-RAY DIFFRACTIONr_scbond_other3.6925.9511047
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8328.7821542
X-RAY DIFFRACTIONr_long_range_B_refined7.99863.6952235
X-RAY DIFFRACTIONr_long_range_B_other7.99963.6972233
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.002→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 33 -
Rwork0.215 602 -
obs--98.76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6733-0.7270.36872.4997-0.87771.3030.13060.13390.0957-0.0280.11310.2023-0.1426-0.2383-0.24370.3227-0.01510.12810.44440.19670.255532.069-32.6071.917
20.58220.2912-0.93050.1678-0.4082.4584-0.0562-0.11780.1065-0.0349-0.03550.1603-0.32790.61240.09160.377-0.09020.05620.49450.11440.585429.044-38.166-2.734
321.240164.524457.1732196.0538173.7127153.9184-0.48990.2731-0.1611-1.69130.9347-0.4926-1.47880.8051-0.44481.3497-0.00370.12351.16780.02880.890725.248-36.763-2.616
46.6048-0.18754.61693.0413-2.87226.1027-0.09680.07860.6516-0.486-0.1933-0.10260.7128-0.10740.29010.5152-0.1336-0.10190.51860.12180.503137.337-54.3812.482
53.15520.0911-1.92951.2674-0.7581.5938-0.10290.39710.06340.19590.0382-0.198-0.0681-0.36960.06470.35420.12580.0370.58090.06830.329128.79-39.486-4.554
67.8503-7.52787.43488.8618-9.627210.96220.71461.29930.5908-0.2119-0.8359-0.2504-0.30910.77370.12130.7801-0.16040.13270.60980.15650.541229.166-19.493-6.644
77.6602-11.0654.433816.3808-8.00749.5489-0.4776-0.24961.24250.88910.5882-1.5793-0.7361-0.6864-0.11050.7858-0.07530.06240.88580.00961.330324.686-42.5437.765
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 295
2X-RAY DIFFRACTION2A301
3X-RAY DIFFRACTION3A302
4X-RAY DIFFRACTION4A308 - 309
5X-RAY DIFFRACTION5A401
6X-RAY DIFFRACTION6A303 - 307
7X-RAY DIFFRACTION7A310 - 313

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