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- PDB-8xc3: Crystal structure of ZmHSL1A-MBQ complex -

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Basic information

Entry
Database: PDB / ID: 8xc3
TitleCrystal structure of ZmHSL1A-MBQ complex
Components2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein
KeywordsOXIDOREDUCTASE / Substrate / Complex
Function / homology
Function and homology information


dioxygenase 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
Chem-92X / 2-OXOGLUTARIC ACID / : / 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsYang, G.-F. / Lin, H.-Y. / Dong, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: An artificially evolved gene for herbicide-resistant rice breeding.
Authors: Dong, J. / Yu, X.H. / Dong, J. / Wang, G.H. / Wang, X.L. / Wang, D.W. / Yan, Y.C. / Xiao, H. / Ye, B.Q. / Lin, H.Y. / Yang, G.F.
History
DepositionDec 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3257
Polymers79,4972
Non-polymers8295
Water10,052558
1
A: 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9533
Polymers39,7481
Non-polymers2052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3724
Polymers39,7481
Non-polymers6233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.580, 54.345, 174.160
Angle α, β, γ (deg.)90.00, 103.96, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein / HPPD Inhibitor Sensitive 1-like 1 protein


Mass: 39748.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: 100285776
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B6U9L0
#2: Chemical ChemComp-CO / COBALT (II) ION


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


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-92X / 1,5-dimethyl-3-(2-methylphenyl)-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-quinazoline-2,4-dione


Mass: 418.442 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H22N2O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 558 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.53 Å3/Da / Density % sol: 51.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: MES, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.06 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 1.79→45.63 Å / Num. obs: 72978 / % possible obs: 97.2 % / Redundancy: 3.5 % / CC1/2: 0.998 / Net I/σ(I): 11.2
Reflection shellResolution: 1.79→1.82 Å / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2570 / CC1/2: 0.817

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→45.63 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2311 3651 5 %
Rwork0.1979 --
obs0.1996 72978 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.79→45.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5506 0 53 558 6117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065686
X-RAY DIFFRACTIONf_angle_d0.8327708
X-RAY DIFFRACTIONf_dihedral_angle_d23.7052156
X-RAY DIFFRACTIONf_chiral_restr0.054836
X-RAY DIFFRACTIONf_plane_restr0.0051011
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.820.31981350.29112570X-RAY DIFFRACTION93
1.82-1.840.3361390.28042632X-RAY DIFFRACTION99
1.84-1.870.29931360.27352584X-RAY DIFFRACTION97
1.87-1.890.28871430.26332706X-RAY DIFFRACTION99
1.9-1.920.29721380.23622624X-RAY DIFFRACTION98
1.92-1.960.28591390.23282640X-RAY DIFFRACTION98
1.96-1.990.24931400.23082651X-RAY DIFFRACTION99
1.99-2.030.26111370.23062597X-RAY DIFFRACTION98
2.03-2.070.28251400.22542694X-RAY DIFFRACTION99
2.07-2.110.27521400.22122644X-RAY DIFFRACTION98
2.11-2.150.24361390.22442648X-RAY DIFFRACTION99
2.15-2.20.27571410.22162663X-RAY DIFFRACTION98
2.2-2.260.28391380.21462632X-RAY DIFFRACTION98
2.26-2.320.25121430.21382721X-RAY DIFFRACTION99
2.32-2.390.23821370.21672594X-RAY DIFFRACTION98
2.39-2.460.27181420.22082709X-RAY DIFFRACTION99
2.46-2.550.23981430.22582701X-RAY DIFFRACTION99
2.55-2.650.25751380.2022630X-RAY DIFFRACTION99
2.65-2.780.26611410.19632664X-RAY DIFFRACTION99
2.78-2.920.27691410.21312679X-RAY DIFFRACTION99
2.92-3.10.23811420.20152702X-RAY DIFFRACTION99
3.11-3.340.20961430.19522709X-RAY DIFFRACTION99
3.35-3.680.21951430.17572722X-RAY DIFFRACTION99
3.68-4.210.19691420.16042701X-RAY DIFFRACTION99
4.21-5.310.16441440.15412725X-RAY DIFFRACTION99
5.31-45.630.1871470.1822785X-RAY DIFFRACTION98

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