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- PDB-9l50: The ring expansion oxygenase SpoC in complex with Mn and N-oxalyl... -

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Basic information

Entry
Database: PDB / ID: 9l50
TitleThe ring expansion oxygenase SpoC in complex with Mn and N-oxalylglycine (NOG)
Componentsring expansion oxygenase SpoC
KeywordsOXIDOREDUCTASE / Ring expansion / Structural basis / Non-heme iron enzymes / Tropolone biosynthesis / Radical rearrangements
Function / homology: / N-OXALYLGLYCINE
Function and homology information
Biological speciesSporormiella sp. (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLiu, M. / He, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2020YFA0803201 China
CitationJournal: To Be Published
Title: The structure of the ring expansion oxygenase SpoC
Authors: Liu, M. / He, X.
History
DepositionDec 21, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ring expansion oxygenase SpoC
B: ring expansion oxygenase SpoC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8269
Polymers82,1452
Non-polymers6807
Water10,016556
1
A: ring expansion oxygenase SpoC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4595
Polymers41,0731
Non-polymers3864
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ring expansion oxygenase SpoC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3674
Polymers41,0731
Non-polymers2943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.412, 84.297, 104.144
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein ring expansion oxygenase SpoC


Mass: 41072.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sporormiella sp. (fungus) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5NO5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / 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: 2.39 Å3/Da / Density % sol: 43.45 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 19% (w/v) PEG 3350, 100 mM sodium citrate, 100 mM Hepes

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 31, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 61974 / % possible obs: 99.9 % / Redundancy: 11.9 % / Biso Wilson estimate: 28.4 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.05 / Net I/σ(I): 9.5
Reflection shellResolution: 1.85→1.96 Å / Num. unique obs: 9825 / CC1/2: 0.594 / Rpim(I) all: 0.68

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→39.07 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2723 3068 4.95 %
Rwork0.2331 --
obs0.2351 61945 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→39.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4954 0 40 556 5550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075173
X-RAY DIFFRACTIONf_angle_d0.8887027
X-RAY DIFFRACTIONf_dihedral_angle_d13.9581940
X-RAY DIFFRACTIONf_chiral_restr0.054747
X-RAY DIFFRACTIONf_plane_restr0.008927
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.880.36721240.33262569X-RAY DIFFRACTION97
1.88-1.910.34911480.30482635X-RAY DIFFRACTION100
1.91-1.940.33261330.282662X-RAY DIFFRACTION100
1.94-1.980.31521740.26122607X-RAY DIFFRACTION100
1.98-2.010.30791240.24872679X-RAY DIFFRACTION100
2.01-2.050.31341350.24272639X-RAY DIFFRACTION100
2.05-2.10.22971360.23862648X-RAY DIFFRACTION100
2.1-2.150.2931260.2412661X-RAY DIFFRACTION100
2.15-2.20.32531510.23182654X-RAY DIFFRACTION100
2.2-2.260.28971320.23142680X-RAY DIFFRACTION100
2.26-2.330.26391280.23722655X-RAY DIFFRACTION100
2.33-2.40.3221280.23982674X-RAY DIFFRACTION100
2.4-2.490.30681400.23292691X-RAY DIFFRACTION100
2.49-2.590.2741230.24232647X-RAY DIFFRACTION100
2.59-2.710.2671130.23672729X-RAY DIFFRACTION100
2.71-2.850.28971440.24552670X-RAY DIFFRACTION100
2.85-3.030.27391420.24282679X-RAY DIFFRACTION100
3.03-3.260.26011250.23922710X-RAY DIFFRACTION100
3.26-3.590.26181570.22412693X-RAY DIFFRACTION100
3.59-4.110.25981580.21082690X-RAY DIFFRACTION100
4.11-5.170.24391480.20672755X-RAY DIFFRACTION100
5.17-39.070.25441790.23582850X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 21.0331 Å / Origin y: -0.5435 Å / Origin z: 7.4755 Å
111213212223313233
T0.2543 Å20.0101 Å2-0.0048 Å2-0.159 Å20.0098 Å2--0.2236 Å2
L1.384 °20.0939 °2-0.3977 °2-0.0927 °2-0.0264 °2--0.5366 °2
S-0.0289 Å °-0.0322 Å °-0.054 Å °0.0075 Å °0.0087 Å °-0.0052 Å °0.0322 Å °0.0107 Å °0.0201 Å °
Refinement TLS groupSelection details: all

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