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- PDB-8x7d: Crystal structure of OsHSL1 L204F/F298L/I335F -

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Basic information

Entry
Database: PDB / ID: 8x7d
TitleCrystal structure of OsHSL1 L204F/F298L/I335F
ComponentsHPPD Inhibitor Sensitive 1-like 1 protein
KeywordsOXIDOREDUCTASE / Complex / substrate
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: 2.2 Å
AuthorsLin, H.-Y. / Dong, J. / Yang, G.-F.
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
DepositionNov 23, 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

Downloads & links

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Assembly

Deposited unit
A: HPPD Inhibitor Sensitive 1-like 1 protein
B: HPPD Inhibitor Sensitive 1-like 1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7378
Polymers80,0342
Non-polymers7026
Water3,207178
1
A: HPPD Inhibitor Sensitive 1-like 1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3684
Polymers40,0171
Non-polymers3513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HPPD Inhibitor Sensitive 1-like 1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3684
Polymers40,0171
Non-polymers3513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.019, 140.474, 58.976
Angle α, β, γ (deg.)90.00, 111.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HPPD Inhibitor Sensitive 1-like 1 protein / Os06g0176700 protein


Mass: 40017.176 Da / Num. of mol.: 2 / Mutation: L204F, F298L, I335F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: OsHSL1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8H620
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Co
#3: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C5H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.22 Å3/Da / Density % sol: 44.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: Bis-Tris, PEG 3350, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→54.63 Å / Num. obs: 32559 / % possible obs: 92.7 % / Redundancy: 5.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.3
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 4 / Num. unique obs: 1923 / CC1/2: 0.863 / % possible all: 98.2

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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: 2.2→31.55 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2483 1996 6.13 %
Rwork0.2105 --
obs0.2128 32559 92.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→31.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5561 0 42 178 5781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025721
X-RAY DIFFRACTIONf_angle_d0.5037762
X-RAY DIFFRACTIONf_dihedral_angle_d28.7462144
X-RAY DIFFRACTIONf_chiral_restr0.04836
X-RAY DIFFRACTIONf_plane_restr0.0031045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.29511320.26011923X-RAY DIFFRACTION83
2.26-2.320.29861520.26292283X-RAY DIFFRACTION96
2.32-2.380.2851430.26432309X-RAY DIFFRACTION98
2.38-2.460.30961570.26082294X-RAY DIFFRACTION98
2.46-2.550.33271450.262330X-RAY DIFFRACTION98
2.55-2.650.31181490.26862258X-RAY DIFFRACTION98
2.65-2.770.27911200.24741876X-RAY DIFFRACTION79
2.77-2.920.29661530.26052314X-RAY DIFFRACTION98
2.92-3.10.27651520.24242314X-RAY DIFFRACTION98
3.1-3.340.27191520.22272317X-RAY DIFFRACTION98
3.34-3.660.20331120.20561804X-RAY DIFFRACTION79
3.68-4.20.20471320.17611970X-RAY DIFFRACTION84
4.21-5.290.19531470.15632287X-RAY DIFFRACTION97
5.3-31.550.22651500.17332284X-RAY DIFFRACTION95

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