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- PDB-6kwb: AtDAO1(dioxygenase for auxin oxidation 1 from Arabidopsis thalian... -

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Basic information

Entry
Database: PDB / ID: 6kwb
TitleAtDAO1(dioxygenase for auxin oxidation 1 from Arabidopsis thaliana) - 2-oxoglutarate binray complex
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-OXOGLUTARIC ACID / 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: 2.5183927715 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)91,7606
Polymers91,5653
Non-polymers1953
Water21612
1
A: 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6923
Polymers30,5221
Non-polymers1702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-6 kcal/mol
Surface area12690 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 area12630 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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.88, 76.799, 166.292
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
11METMETASNASNchain 'A'AA8 - 851 - 78
12GLUGLUHISHISchain 'A'AA89 - 16282 - 155
13LEULEUASNASNchain 'A'AA175 - 190168 - 183
14GLUGLUASPASPchain 'A'AA195 - 198188 - 191
15SERSERHISHISchain 'A'AA201 - 235194 - 228
16TYRTYRASPASPchain 'A'AA246 - 268239 - 261
21METMETASNASNchain 'B'BB8 - 851 - 78
22GLUGLUHISHISchain 'B'BB89 - 16282 - 155
23LEULEUASNASNchain 'B'BB175 - 190168 - 183
24GLUGLUASPASPchain 'B'BB195 - 198188 - 191
25SERSERHISHISchain 'B'BB201 - 235194 - 228
26TYRTYRASPASPchain 'B'BB246 - 268239 - 261
31METMETASNASNchain 'C'CC8 - 851 - 78
32GLUGLUHISHISchain 'C'CC89 - 16282 - 155
33LEULEUASNASNchain 'C'CC175 - 190168 - 183
34GLUGLUASPASPchain 'C'CC195 - 198188 - 191
35SERSERHISHISchain 'C'CC201 - 235194 - 228
36TYRTYRASPASPchain 'C'CC246 - 268239 - 261

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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: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


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


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: 0.03M 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: 2.48→50 Å / Num. obs: 34716 / % possible obs: 98.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 70.8723491824 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.126 / Net I/σ(I): 11.6
Reflection shellResolution: 2.48→2.57 Å / Rmerge(I) obs: 3.77 / Num. unique obs: 3206 / CC1/2: 0.5

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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: 6KWA

6kwa


Resolution: 2.5183927715→28.2078242366 Å / SU ML: 0.416181155805 / Cross valid method: FREE R-VALUE / σ(F): 1.3255267704 / Phase error: 33.2812877571
RfactorNum. reflection% reflection
Rfree0.281531009251 1993 6.03573591763 %
Rwork0.224639577674 31027 -
obs0.22810200341 33020 98.16862885 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.0462275556 Å2
Refinement stepCycle: LAST / Resolution: 2.5183927715→28.2078242366 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6043 0 12 12 6067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01006922580766178
X-RAY DIFFRACTIONf_angle_d1.488534455388364
X-RAY DIFFRACTIONf_chiral_restr0.0635050429927925
X-RAY DIFFRACTIONf_plane_restr0.008229147683171093
X-RAY DIFFRACTIONf_dihedral_angle_d14.81398079852300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5184-2.58130.3507845417841180.3165244612631830X-RAY DIFFRACTION82.4375793483
2.5813-2.65110.3401452530121450.3258672928422223X-RAY DIFFRACTION99.7472620051
2.6511-2.7290.4129426806341440.3208741208472226X-RAY DIFFRACTION99.915682968
2.729-2.8170.4445347646231400.3086757992852217X-RAY DIFFRACTION99.8305802626
2.817-2.91760.3701201892071430.3081584234062226X-RAY DIFFRACTION99.8735244519
2.9176-3.03430.3866767683311430.3046877204042221X-RAY DIFFRACTION99.8310810811
3.0343-3.17220.3697029080621400.2895577880992245X-RAY DIFFRACTION99.9580888516
3.1722-3.33920.3131214064711450.2728051027232237X-RAY DIFFRACTION99.958036089
3.3392-3.54810.3167283431461450.2465767476542217X-RAY DIFFRACTION99.9153976311
3.5481-3.82140.2938509136131420.2400226207352280X-RAY DIFFRACTION99.9587288485
3.8214-4.20480.3098842559551450.209210818572240X-RAY DIFFRACTION99.3336109954
4.2048-4.81070.2457175085941460.1755397877062281X-RAY DIFFRACTION99.6714579055
4.8107-6.05110.271308715771510.2053167154122294X-RAY DIFFRACTION99.8366680278
6.0511-28.2070.1956596103261460.1851932353512290X-RAY DIFFRACTION94.2724458204

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