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- PDB-9gi5: Fe(II)-2-oxoglutarate-dependent Oryza sativa dioxygenase HSL1 in ... -

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Basic information

Entry
Database: PDB / ID: 9gi5
TitleFe(II)-2-oxoglutarate-dependent Oryza sativa dioxygenase HSL1 in complex with 2-oxoglutarate
ComponentsOs06g0176700 protein
KeywordsOXIDOREDUCTASE / Herbicide resistance / HPPD-inhibitor insensitive / 2-oxoglutarate oxygenase
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 / : / Os06g0176700 protein
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsDhingra, S. / Alshref, F.M. / Farcas, I. / Allen, M.D. / Brewitz, L. / 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 HSL1 in complex with 2-oxoglutarate
Authors: Dhingra, S. / Alshref, F.M. / Farcas, I. / Allen, M.D. / Brewitz, L. / Schofield, C.J.
History
DepositionAug 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Os06g0176700 protein
B: Os06g0176700 protein
C: Os06g0176700 protein
D: Os06g0176700 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,06518
Polymers161,6434
Non-polymers1,42314
Water4,071226
1
A: Os06g0176700 protein
D: Os06g0176700 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4978
Polymers80,8212
Non-polymers6766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Os06g0176700 protein
C: Os06g0176700 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,56810
Polymers80,8212
Non-polymers7478
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.671, 102.593, 156.058
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Os06g0176700 protein / Os06g0178500 protein / Putative Fe(II)/2-oxoglutarate-dependent oxygenase


Mass: 40410.656 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice)
Gene: OsHSL1, LOC_Os06g07932, LOC_Os06g08032, Os06g0176700, Os06g0178500, OSNPB_060176700, OSNPB_060178500
Production host: Escherichia coli (E. coli) / Strain (production host): PLys Y / References: UniProt: Q8H620

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Non-polymers , 5 types, 240 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.25 Å3/Da / Density % sol: 45.28 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 20% v/v PEG 500* MME; 10% w/v PEG 20000 0.1M Sodium HEPES; MOPS (acid), pH 7.5 0.06M Magnesium chloride hexahydrate; 0.06M Calcium chloride dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 31, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.35→51.99 Å / Num. obs: 60655 / % possible obs: 99.9 % / Redundancy: 13.7 % / Biso Wilson estimate: 45.71 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.057 / Rrim(I) all: 0.154 / Net I/σ(I): 12.9
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 13.1 % / Rmerge(I) obs: 1.472 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4415 / CC1/2: 0.688 / Rpim(I) all: 0.608 / Rrim(I) all: 1.595 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→51.3 Å / SU ML: 0.2811 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.7582
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2326 3007 4.97 %
Rwork0.1975 57555 -
obs0.1993 60562 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.49 Å2
Refinement stepCycle: LAST / Resolution: 2.35→51.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11220 0 78 226 11524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004211708
X-RAY DIFFRACTIONf_angle_d0.685815898
X-RAY DIFFRACTIONf_chiral_restr0.04441694
X-RAY DIFFRACTIONf_plane_restr0.00792147
X-RAY DIFFRACTIONf_dihedral_angle_d7.89941636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.390.27791400.26632621X-RAY DIFFRACTION97.36
2.39-2.430.3331440.26192731X-RAY DIFFRACTION99.76
2.43-2.470.28161520.26482661X-RAY DIFFRACTION99.65
2.47-2.520.33041220.25322726X-RAY DIFFRACTION99.62
2.52-2.570.27261220.25162745X-RAY DIFFRACTION99.83
2.57-2.630.31781370.25652721X-RAY DIFFRACTION99.93
2.63-2.690.27131500.24832683X-RAY DIFFRACTION99.96
2.69-2.760.30921410.25952724X-RAY DIFFRACTION100
2.76-2.830.27941310.2392749X-RAY DIFFRACTION99.97
2.83-2.910.30211480.23422702X-RAY DIFFRACTION99.96
2.91-3.010.25941480.22782739X-RAY DIFFRACTION100
3.01-3.120.25011340.22252729X-RAY DIFFRACTION100
3.12-3.240.251240.21552764X-RAY DIFFRACTION99.97
3.24-3.390.27731390.2242738X-RAY DIFFRACTION100
3.39-3.570.21391390.18542753X-RAY DIFFRACTION100
3.57-3.790.23741440.17852755X-RAY DIFFRACTION100
3.79-4.080.18981540.17632744X-RAY DIFFRACTION99.86
4.08-4.490.20581560.15512758X-RAY DIFFRACTION99.73
4.49-5.140.18771620.16482760X-RAY DIFFRACTION99.62
5.14-6.480.23781590.19242821X-RAY DIFFRACTION100
6.48-51.30.1921610.16662931X-RAY DIFFRACTION99.71
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.407600947770.7854887904720.2443545905382.69496969303-0.08666027027611.779273118090.1091190330480.06141856703270.09896720168390.16358097251-0.0700616365270.03030334118240.0057762251240.160192740683-0.04003038454910.2551716920590.008356234150410.01717806036080.2216123733540.03221491691940.19055405457-7.0912575926219.0735829254-40.0893615278
21.67940392924-0.344929213327-0.5761527414952.136466269620.002216902385873.2373128421-0.08676905346470.00514341512481-0.0425892549510.1936403824040.04479817006960.2892308913280.204513616914-0.3055284240460.0542065835470.298132154955-0.001063756854410.04015634778810.2515472425850.02319540176210.26071567134-21.7740798588-0.972070558588-3.09040695278
32.02669037255-0.598248506578-0.6183863253013.412033615311.242341082122.839041716990.020276452536-0.1339928236520.161464604330.2143661054720.421248442458-0.8108405600660.1257631381890.786598291046-0.1758290971140.3312180850790.0178915207857-0.1409894119070.499643463544-0.1750190075350.47676363076219.4575634547-2.01407633805-2.62760920487
44.69151245924-0.2241363171371.151163683091.644582413340.2873628987022.860139799710.11723543412-0.6823401648710.1102635024920.1077618717780.09439744028971.04187634187-0.0313042190965-1.38299742189-0.07254745004950.5386440192690.06053402067850.05937063924951.020081835420.1405110988851.17293235891-47.754962411122.7039430905-37.983544471
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
11chain AAA - C3 - 402
22chain BBD - F3 - 402
33chain CCG - I3 - 402
44chain DDJ - L4 - 402

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