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- PDB-8x7c: Crystal structure of ZmHSL1A -

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Basic information

Entry
Database: PDB / ID: 8x7c
TitleCrystal structure of ZmHSL1A
Components2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein
KeywordsOXIDOREDUCTASE / Complex / Enzyme
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
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: 1.597 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

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Assembly

Deposited unit
B: 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein
A: 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9076
Polymers79,4972
Non-polymers4104
Water18,2131011
1
B: 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
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
Unit cell
Length a, b, c (Å)88.062, 54.368, 174.744
Angle α, β, γ (deg.)90.00, 104.34, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1011 / Source method: isolated from a natural source / Formula: H2O

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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: 2.55 Å3/Da / Density % sol: 51.75 %
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: Jun 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 1.597→30 Å / Num. obs: 106167 / % possible obs: 99.4 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Net I/σ(I): 16.33
Reflection shellResolution: 1.6→1.62 Å / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 2.68 / Num. unique obs: 3167 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.597→26.84 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2037 5309 5 %
Rwork0.1735 --
obs0.175 106167 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.597→26.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5536 0 22 1016 6574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065689
X-RAY DIFFRACTIONf_angle_d0.8147702
X-RAY DIFFRACTIONf_dihedral_angle_d6.0454153
X-RAY DIFFRACTIONf_chiral_restr0.052834
X-RAY DIFFRACTIONf_plane_restr0.0051015
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5971-1.61520.24451670.22773167X-RAY DIFFRACTION94
1.6152-1.63420.24041760.22123331X-RAY DIFFRACTION100
1.6342-1.65410.2411760.21043346X-RAY DIFFRACTION100
1.6541-1.67510.22671770.2143357X-RAY DIFFRACTION100
1.6751-1.69710.24931750.20143335X-RAY DIFFRACTION100
1.6971-1.72040.24011780.19723387X-RAY DIFFRACTION100
1.7204-1.74490.22531750.19523315X-RAY DIFFRACTION100
1.7449-1.7710.22191770.19243355X-RAY DIFFRACTION100
1.771-1.79860.22931760.19783346X-RAY DIFFRACTION100
1.7986-1.82810.21821760.18253342X-RAY DIFFRACTION100
1.8281-1.85960.22561780.19033385X-RAY DIFFRACTION100
1.8596-1.89340.21121760.18873335X-RAY DIFFRACTION100
1.8934-1.92980.22231770.19063376X-RAY DIFFRACTION100
1.9298-1.96920.20811760.18583340X-RAY DIFFRACTION100
1.9692-2.0120.20821790.18593391X-RAY DIFFRACTION100
2.012-2.05880.19431760.18543346X-RAY DIFFRACTION100
2.0588-2.11030.2261760.18063346X-RAY DIFFRACTION100
2.1103-2.16730.21041770.18523381X-RAY DIFFRACTION100
2.1673-2.23110.22021760.17843356X-RAY DIFFRACTION100
2.2311-2.3030.20041760.17723336X-RAY DIFFRACTION100
2.303-2.38530.23831790.17593396X-RAY DIFFRACTION100
2.3853-2.48070.22691770.18063373X-RAY DIFFRACTION100
2.4807-2.59360.23511800.18763412X-RAY DIFFRACTION100
2.5936-2.73020.2081770.17623365X-RAY DIFFRACTION100
2.7302-2.9010.2031770.17743355X-RAY DIFFRACTION100
2.901-3.12470.20251770.17523376X-RAY DIFFRACTION100
3.1247-3.43860.18881800.16613422X-RAY DIFFRACTION100
3.4386-3.93480.15261770.15053355X-RAY DIFFRACTION99
3.9348-4.95240.18891800.13993418X-RAY DIFFRACTION100
4.9524-26.840.19521850.17043513X-RAY DIFFRACTION100

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