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- PDB-6d3h: FT_T dioxygenase with bound dichlorprop -

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Basic information

Entry
Database: PDB / ID: 6d3h
TitleFT_T dioxygenase with bound dichlorprop
ComponentsFT_T dioxygenase
KeywordsOXIDOREDUCTASE / Alpha-ketoglutarate-dependent dioxygenase
Function / homology
Function and homology information


(R)-dichlorprop dioxygenase (2-oxoglutarate) / taurine dioxygenase activity / sulfur compound metabolic 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 / : / (2R)-2-(2,4-dichlorophenoxy)propanoic acid / (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase
Similarity search - Component
Biological speciesSphingobium herbicidovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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
I: FT_T dioxygenase
M: FT_T dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,68920
Polymers133,7874
Non-polymers1,90216
Water18,1591008
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)135,68920
Polymers133,7874
Non-polymers1,90216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
Buried area8460 Å2
ΔGint-88 kcal/mol
Surface area44060 Å2
MethodPISA
2
I: FT_T dioxygenase
M: FT_T dioxygenase
hetero molecules

I: FT_T dioxygenase
M: FT_T dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,68920
Polymers133,7874
Non-polymers1,90216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Buried area8500 Å2
ΔGint-84 kcal/mol
Surface area44210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.161, 138.161, 148.518
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11B-659-

HOH

21M-661-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31I
41M

NCS domain segments:

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-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB
33IC
44MD

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Components

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Protein , 1 types, 4 molecules ABIM

#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) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KSC8*PLUS

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Non-polymers , 5 types, 1024 molecules

#2: Chemical
ChemComp-FTV / (2R)-2-(2,4-dichlorophenoxy)propanoic acid


Mass: 235.064 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H8Cl2O3
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#4: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1008 / 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: 3.14 Å3/Da / Density % sol: 60.79 %
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 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.03→119.65 Å / Num. obs: 103868 / % possible obs: 99.9 % / Redundancy: 10.8 % / Rsym value: 0.12 / Net I/σ(I): 27.4
Reflection shellResolution: 2.03→2.07 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.57 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→46.6 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.126 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.141
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2113 5183 5 %RANDOM
Rwork0.1701 ---
obs0.1722 98641 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 69.84 Å2 / Biso mean: 26.981 Å2 / Biso min: 12.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0.18 Å20 Å2
2---0.35 Å20 Å2
3---0.53 Å2
Refinement stepCycle: final / Resolution: 2.03→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9163 0 104 1008 10275
Biso mean--25.84 36.5 -
Num. residues----1145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0229524
X-RAY DIFFRACTIONr_angle_refined_deg2.0311.94612970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75951153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55323.348457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.451151514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8551572
X-RAY DIFFRACTIONr_chiral_restr0.2430.21416
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217396
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1139MEDIUM POSITIONAL0.060.5
2B1139MEDIUM POSITIONAL0.060.5
3I1139MEDIUM POSITIONAL0.060.5
4M1139MEDIUM POSITIONAL0.060.5
1A1134LOOSE POSITIONAL0.285
2B1134LOOSE POSITIONAL0.275
3I1134LOOSE POSITIONAL0.245
4M1134LOOSE POSITIONAL0.255
1A1139MEDIUM THERMAL0.942
2B1139MEDIUM THERMAL0.952
3I1139MEDIUM THERMAL0.872
4M1139MEDIUM THERMAL0.882
1A1134LOOSE THERMAL1.1610
2B1134LOOSE THERMAL1.210
3I1134LOOSE THERMAL1.1810
4M1134LOOSE THERMAL1.2110
LS refinement shellResolution: 2.03→2.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 383 -
Rwork0.194 7009 -
all-7392 -
obs--96.29 %

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