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- PDB-6kwa: AtDAO1(dioxygenase for auxin oxidation 1 from Arabidopsis thaliana) -

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Basic information

Entry
Database: PDB / ID: 6kwa
TitleAtDAO1(dioxygenase for auxin oxidation 1 from Arabidopsis thaliana)
Components2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein
KeywordsOXIDOREDUCTASE / auxin / oxidation / 2-oxoglutarate/Fe(II)-dependent oxygenase / IAA / oxIAA / dsbh fold / plant hormone
Function / homology
Function and homology information


indole-3-acetaldehyde oxidase activity / auxin catabolic process / dioxygenase activity / nucleus / metal ion binding / cytoplasm
Similarity search - Function
: / Non-haem dioxygenase N-terminal domain / non-haem dioxygenase in morphine synthesis N-terminal / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile.
Similarity search - Domain/homology
2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09429141431 Å
AuthorsRhee, S. / Jin, S. / Lee, H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
Rural Development Administrationpj01325801 Korea, Republic Of
National Research Foundation (NRF, Korea)2017r1a2b4002860 Korea, Republic Of
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Crystal structure of the indole-3-acetic acid-catabolizing enzyme DAO1 from Arabidopsis thaliana.
Authors: Jin, S.H. / Lee, H. / Shin, Y. / Kim, J.H. / Rhee, S.
History
DepositionSep 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein
B: 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein
C: 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6145
Polymers91,5653
Non-polymers492
Water1,00956
1
A: 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5462
Polymers30,5221
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-7 kcal/mol
Surface area12640 Å2
MethodPISA
2
B: 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5462
Polymers30,5221
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-8 kcal/mol
Surface area12860 Å2
MethodPISA
3
C: 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein


Theoretical massNumber of molelcules
Total (without water)30,5221
Polymers30,5221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.626, 75.547, 165.318
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLUGLUchain 'A'AA8 - 311 - 24
12CYSCYSPHEPHEchain 'A'AA35 - 16328 - 156
13GLNGLNVALVALchain 'A'AA174 - 191167 - 184
14LEULEUMETMETchain 'A'AA194 - 197187 - 190
15LEULEUARGARGchain 'A'AA210 - 236203 - 229
16THRTHRGLUGLUchain 'A'AA243 - 265236 - 258
21METMETGLUGLUchain 'B'BB8 - 311 - 24
22CYSCYSPHEPHEchain 'B'BB35 - 16328 - 156
23GLNGLNVALVALchain 'B'BB174 - 191167 - 184
24LEULEUMETMETchain 'B'BB194 - 197187 - 190
25LEULEUARGARGchain 'B'BB210 - 236203 - 229
26THRTHRGLUGLUchain 'B'BB243 - 265236 - 258
31METMETGLUGLUchain 'C'CC8 - 311 - 24
32CYSCYSPHEPHEchain 'C'CC35 - 16328 - 156
33GLNGLNVALVALchain 'C'CC174 - 191167 - 184
34LEULEUMETMETchain 'C'CC194 - 197187 - 190
35LEULEUARGARGchain 'C'CC210 - 236203 - 229
36THRTHRGLUGLUchain 'C'CC243 - 265236 - 258

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Components

#1: Protein 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein / F7A19.21 protein / Putative dioxygenase


Mass: 30521.697 Da / Num. of mol.: 3 / Fragment: UNP residues 9-277
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g14130, At1g14130/F7A19_21, F7A19.21, F7A19_21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XI75
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.61 Å3/Da / Density % sol: 52.93 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: 30mM KH2PO4, 16% PEG 8000, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 56807 / % possible obs: 96.4 % / Redundancy: 7.2 % / Biso Wilson estimate: 50.1445005062 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Net I/σ(I): 11.7
Reflection shellResolution: 2.08→2.16 Å / Rmerge(I) obs: 1.67 / Num. unique obs: 3898 / CC1/2: 0.472

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C3Q, 2BRT

5c3q

2brt


Resolution: 2.09429141431→33.8805234655 Å / SU ML: 0.300742786836 / Cross valid method: FREE R-VALUE / σ(F): 1.33437384029 / Phase error: 33.4052762107
RfactorNum. reflection% reflection
Rfree0.281503483539 2001 3.52425235126 %
Rwork0.242417305459 54777 -
obs0.243821334415 56778 99.1547623206 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.6320309229 Å2
Refinement stepCycle: LAST / Resolution: 2.09429141431→33.8805234655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6025 0 2 56 6083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009594951600136149
X-RAY DIFFRACTIONf_angle_d1.375324036768323
X-RAY DIFFRACTIONf_chiral_restr0.0569395993051923
X-RAY DIFFRACTIONf_plane_restr0.007412618222251084
X-RAY DIFFRACTIONf_dihedral_angle_d13.20187455312295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0943-2.14670.3513860557121330.33809380683647X-RAY DIFFRACTION93.4025203855
2.1467-2.20470.3994163902951400.338382524323872X-RAY DIFFRACTION100
2.2047-2.26950.3967409134061430.3273693165173874X-RAY DIFFRACTION99.9253731343
2.2695-2.34280.3768835617741480.3192507200963915X-RAY DIFFRACTION99.9262174127
2.3428-2.42650.3259825084441410.3178892465483890X-RAY DIFFRACTION100
2.4265-2.52360.3424240107661430.3050956089453902X-RAY DIFFRACTION99.9258893281
2.5236-2.63840.3790357730331430.2945952835433921X-RAY DIFFRACTION99.9016715831
2.6384-2.77750.3897576428751460.2922193166413903X-RAY DIFFRACTION99.9259624877
2.7775-2.95140.3380705863391390.2893258996883944X-RAY DIFFRACTION99.9265785609
2.9514-3.17910.3528760945081470.2872192712883938X-RAY DIFFRACTION99.9021765713
3.1791-3.49880.3177534550641410.2587376301783951X-RAY DIFFRACTION99.90234375
3.4988-4.00430.2851610873171440.2311904465763987X-RAY DIFFRACTION99.9516090007
4.0043-5.04240.194812280361490.1888035303264013X-RAY DIFFRACTION99.7125059895
5.0424-33.880.2409025459871440.2081180712954020X-RAY DIFFRACTION95.9668126296

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