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- PDB-6d3i: ftv7 dioxygenase with 2,4-D bound -

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Basic information

Entry
Database: PDB / ID: 6d3i
Titleftv7 dioxygenase with 2,4-D bound
Componentsftv7 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 / (2,4-DICHLOROPHENOXY)ACETIC ACID / : / (R)-phenoxypropionate/alpha-ketoglutarate-dioxygenase
Similarity search - Component
Biological speciesSphingobium herbicidovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.196 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 1.3Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ftv7 dioxygenase
G: ftv7 dioxygenase
D: ftv7 dioxygenase
J: ftv7 dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,98914
Polymers133,7274
Non-polymers1,26210
Water82946
1
A: ftv7 dioxygenase
D: ftv7 dioxygenase
hetero molecules

G: ftv7 dioxygenase
J: ftv7 dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,98914
Polymers133,7274
Non-polymers1,26210
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area9610 Å2
ΔGint-95 kcal/mol
Surface area44080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.927, 109.980, 116.145
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
ftv7 dioxygenase


Mass: 33431.730 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
#2: Chemical
ChemComp-CO / COBALT (II) ION


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


Mass: 146.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-CFA / (2,4-DICHLOROPHENOXY)ACETIC ACID / 2,4-DICHLOROPHENOXYACETIC ACID


Mass: 221.037 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H6Cl2O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: -crystallization: Wizard 34 H7 = 30% MPD, 0.1M imidazole-HCl-pH 6.5, 0.2M ammonium sulfate, 10% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→49.8 Å / Num. obs: 20563 / % possible obs: 100 % / Redundancy: 4.8 % / Biso Wilson estimate: 57.27 Å2 / Rsym value: 0.106 / Net I/σ(I): 10.6
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 4.7 % / Num. unique obs: 1037 / Rsym value: 0.506 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.196→49.701 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.273 1985 9.66 %
Rwork0.1762 --
obs0.1858 20548 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.196→49.701 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9128 0 70 46 9244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0159434
X-RAY DIFFRACTIONf_angle_d1.51312844
X-RAY DIFFRACTIONf_dihedral_angle_d16.7195564
X-RAY DIFFRACTIONf_chiral_restr0.0871398
X-RAY DIFFRACTIONf_plane_restr0.0111671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1962-3.27610.3591280.24111162X-RAY DIFFRACTION89
3.2761-3.36470.31091370.21071306X-RAY DIFFRACTION100
3.3647-3.46360.30831330.19671334X-RAY DIFFRACTION100
3.4636-3.57540.29071460.20041310X-RAY DIFFRACTION100
3.5754-3.70320.32121430.19651318X-RAY DIFFRACTION100
3.7032-3.85140.31991370.18981329X-RAY DIFFRACTION100
3.8514-4.02660.30661400.17311320X-RAY DIFFRACTION100
4.0266-4.23880.27551520.15641303X-RAY DIFFRACTION100
4.2388-4.50420.20271360.1371346X-RAY DIFFRACTION100
4.5042-4.85170.21861500.12521333X-RAY DIFFRACTION100
4.8517-5.33940.25261440.15311339X-RAY DIFFRACTION100
5.3394-6.11080.27171410.1791358X-RAY DIFFRACTION100
6.1108-7.69440.27891440.20151365X-RAY DIFFRACTION100
7.6944-49.70680.25841540.18741440X-RAY DIFFRACTION99

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