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- PDB-8s7b: Fe(II)-2-oxoglutarate-dependent Oryza sativa dioxygenase His1 in ... -

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Basic information

Entry
Database: PDB / ID: 8s7b
TitleFe(II)-2-oxoglutarate-dependent Oryza sativa dioxygenase His1 in complex with 2-oxoglutarate
ComponentsFe(II)/2-oxoglutarate-dependent oxygenase
KeywordsOXYGEN BINDING / His1 / HPPD-resistance / oxygenase / 2-oxoglutarate / complex / inhibitor / rice
Function / homology
Function and homology information


oxidoreductase activity / metal ion binding
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 / : / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Fe(II)/2-oxoglutarate-dependent oxygenase
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsDhingra, S. / Alshref, F. / Farcas, I.M. / Brewitz, L. / Allen, M.D. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V001892/1 United Kingdom
CitationJournal: To Be Published
Title: Fe(II)-2-oxoglutarate-dependent Oryza sativa dioxygenase His1 in complex with 2-oxoglutarate
Authors: Dhingra, S. / Alshref, F. / Farcas, I.M. / Brewitz, L. / Allen, M.D. / Schofield, C.J.
History
DepositionFeb 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fe(II)/2-oxoglutarate-dependent oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2244
Polymers40,6531
Non-polymers5713
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.332, 67.432, 83.176
Angle α, β, γ (deg.)90.000, 92.090, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-505-

HOH

21A-506-

HOH

31A-752-

HOH

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Components

#1: Protein Fe(II)/2-oxoglutarate-dependent oxygenase / Os02g0280700 protein / cDNA clone:J013034J09 / full insert sequence


Mass: 40652.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The His-tag was removed by TEV protease before crystallography. Some residues at the N-termini was not visible in the electron density map.
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: HIS1, LOC_Os02g17940, Os02g0280700, OSNPB_020280700 / Plasmid: PET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q6ES21
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.21 Å3/Da / Density % sol: 44.43 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.15 M Magnesium acetate tetrahydrate 0.1 M Sodium citrate 5.6 20 % v/v PEG Smear Broad 15% Glycerol used for collection

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.75→47.98 Å / Num. obs: 38126 / % possible obs: 99.8 % / Redundancy: 7 % / Biso Wilson estimate: 25.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.024 / Rrim(I) all: 0.065 / Net I/σ(I): 18.5
Reflection shellResolution: 1.75→1.878 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.895 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1899 / CC1/2: 0.804 / Rpim(I) all: 0.389 / Rrim(I) all: 0.979 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→47.98 Å / SU ML: 0.1852 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.7367
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2026 1983 5.21 %
Rwork0.1747 36114 -
obs0.1762 38097 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.92 Å2
Refinement stepCycle: LAST / Resolution: 1.75→47.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2821 0 36 252 3109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00372935
X-RAY DIFFRACTIONf_angle_d0.60713969
X-RAY DIFFRACTIONf_chiral_restr0.0451426
X-RAY DIFFRACTIONf_plane_restr0.0051529
X-RAY DIFFRACTIONf_dihedral_angle_d13.60931136
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.36431400.33732557X-RAY DIFFRACTION97.79
1.79-1.840.28741480.27332568X-RAY DIFFRACTION99.56
1.84-1.90.23391430.23172535X-RAY DIFFRACTION99.93
1.9-1.960.24761200.2212575X-RAY DIFFRACTION99.67
1.96-2.030.25471050.20062624X-RAY DIFFRACTION99.82
2.03-2.110.21651670.18112540X-RAY DIFFRACTION99.93
2.11-2.20.23011250.18042603X-RAY DIFFRACTION99.89
2.2-2.320.22991620.17372549X-RAY DIFFRACTION99.93
2.32-2.470.24231650.182521X-RAY DIFFRACTION99.81
2.47-2.660.22061450.18092587X-RAY DIFFRACTION99.53
2.66-2.920.24141180.17942609X-RAY DIFFRACTION100
2.92-3.350.18861220.17032619X-RAY DIFFRACTION100
3.35-4.210.16421820.14972566X-RAY DIFFRACTION99.93
4.22-47.980.17611410.15822661X-RAY DIFFRACTION99.75
Refinement TLS params.Method: refined / Origin x: 20.6140747179 Å / Origin y: 1.39237469669 Å / Origin z: 23.2583054893 Å
111213212223313233
T0.193578109379 Å2-0.0113935308294 Å2-0.0015900728817 Å2-0.150925441845 Å2-0.0227925512927 Å2--0.145852720916 Å2
L1.31763839981 °2-0.591009648164 °2-0.236034349056 °2-1.57930783224 °20.277977235628 °2--1.57955679086 °2
S0.0210192495963 Å °0.243632810417 Å °-0.105632429363 Å °-0.278506454832 Å °-0.0567507389546 Å °0.113501459749 Å °-0.0369391302296 Å °0.0388906313585 Å °0.0336368322102 Å °
Refinement TLS groupSelection details: chain A

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