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- PDB-6d3m: FT_T dioxygenase with bound quizalofop -

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Basic information

Entry
Database: PDB / ID: 6d3m
TitleFT_T dioxygenase with bound quizalofop
ComponentsFT_T dioxygenase
KeywordsOXIDOREDUCTASE / Alpha-ketoglutarate-dependent dioxygenase
Function / homology
Function and homology information


(R)-dichlorprop dioxygenase (2-oxoglutarate) / : / 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-FTJ / (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase
Similarity search - Component
Biological speciesSphingobium herbicidovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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 / 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: FT_T dioxygenase
B: FT_T dioxygenase
F: FT_T dioxygenase
J: FT_T dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,05718
Polymers133,7874
Non-polymers2,27014
Water13,673759
1
A: FT_T dioxygenase
B: FT_T dioxygenase
hetero molecules

A: FT_T dioxygenase
B: FT_T dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,05718
Polymers133,7874
Non-polymers2,27014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
Buried area8310 Å2
ΔGint-88 kcal/mol
Surface area43960 Å2
MethodPISA
2
F: FT_T dioxygenase
J: FT_T dioxygenase
hetero molecules

F: FT_T dioxygenase
J: FT_T dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,05718
Polymers133,7874
Non-polymers2,27014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
Buried area8440 Å2
ΔGint-85 kcal/mol
Surface area44050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.778, 137.778, 148.346
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31F
41J

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 5 / Auth seq-ID: 11 - 295 / Label seq-ID: 11 - 295

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3FC
4JD

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Components

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Protein , 1 types, 4 molecules ABFJ

#1: Protein
FT_T dioxygenase


Mass: 33446.809 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: engineered variant / Source: (gene. exp.) Sphingobium herbicidovorans (bacteria) / Gene: rdpA / Production host: Escherichia coli (E. coli)
References: UniProt: Q8KSC8*PLUS, (R)-dichlorprop dioxygenase (2-oxoglutarate)

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Non-polymers , 5 types, 773 molecules

#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-FTJ / (2R)-2-{4-[(6-chloroquinoxalin-2-yl)oxy]phenoxy}propanoic acid


Mass: 344.749 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H13ClN2O4
#4: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6O5
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 759 / 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: 3.06 Å3/Da / Density % sol: 59.83 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: The precipitant solution is 2.5 M NaCl, 0.1M KP04/NaP04-pH 6.2; the protein solution is 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 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.03→119.4 Å / Num. obs: 102415 / % possible obs: 99.6 % / Redundancy: 7.8 % / Rsym value: 0.155 / Net I/σ(I): 16.5
Reflection shellResolution: 2.03→2.07 Å / Num. unique obs: 5147 / Rsym value: 0.495 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→45.1 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.623 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.145 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2172 5110 5 %RANDOM
Rwork0.1774 ---
obs0.17941 97268 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 38.306 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.1 Å20 Å2
2--0.21 Å20 Å2
3----0.31 Å2
Refinement stepCycle: 1 / Resolution: 2.03→45.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9148 0 142 759 10049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0229566
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8561.95113032
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.78351153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34123.362458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.211151511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6681572
X-RAY DIFFRACTIONr_chiral_restr0.1810.21414
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217444
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.1411.55727
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.01129327
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.23433839
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.1054.53699
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A1135medium positional0.070.5
B1135medium positional0.070.5
F1135medium positional0.070.5
J1135medium positional0.070.5
A1130loose positional0.215
B1130loose positional0.215
F1130loose positional0.215
J1130loose positional0.235
A1135medium thermal1.082
B1135medium thermal1.082
F1135medium thermal12
J1135medium thermal0.992
A1130loose thermal1.2210
B1130loose thermal1.2110
F1130loose thermal1.1810
J1130loose thermal1.210
LS refinement shellResolution: 2.03→2.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 360 -
Rwork0.238 6787 -
obs--94 %

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