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- PDB-9l51: The structure of the ring expansion oxygenase SpoC -

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Basic information

Entry
Database: PDB / ID: 9l51
TitleThe structure of the ring expansion oxygenase SpoC
Componentsring expansion oxygenase SpoC
KeywordsOXIDOREDUCTASE / Ring expansion / Structural basis / Non-heme iron enzymes / Tropolone biosynthesis / Radical rearrangements
Function / homology:
Function and homology information
Biological speciesSporormiella sp. (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)83,0536
Polymers82,8702
Non-polymers1834
Water9,872548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-53 kcal/mol
Surface area27120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.443, 84.993, 104.631
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ring expansion oxygenase SpoC


Mass: 41435.145 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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 2.18 Å3/Da / Density % sol: 43.71 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 18% (w/v) PEG 3350, 100 mM sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 55037 / % possible obs: 95.3 % / Redundancy: 7.6 % / CC1/2: 0.984 / Rpim(I) all: 0.05 / Net I/σ(I): 12
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 2614 / CC1/2: 0.386 / Rpim(I) all: 0.25

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→42.5 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 27.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2498 2725 5.26 %
Rwork0.2073 --
obs0.2096 51794 89.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→42.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4836 0 4 548 5388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064995
X-RAY DIFFRACTIONf_angle_d0.9076787
X-RAY DIFFRACTIONf_dihedral_angle_d5.699662
X-RAY DIFFRACTIONf_chiral_restr0.054730
X-RAY DIFFRACTIONf_plane_restr0.007888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.3398880.33011439X-RAY DIFFRACTION51
1.94-1.970.41331120.31871845X-RAY DIFFRACTION66
1.97-2.010.29451270.30742162X-RAY DIFFRACTION76
2.01-2.060.31991060.28582160X-RAY DIFFRACTION76
2.06-2.110.31411280.27592467X-RAY DIFFRACTION86
2.11-2.160.29781560.26872559X-RAY DIFFRACTION91
2.16-2.220.26931330.25292648X-RAY DIFFRACTION92
2.22-2.280.27651310.23442667X-RAY DIFFRACTION93
2.28-2.360.32391660.22962686X-RAY DIFFRACTION95
2.36-2.440.28791570.21052690X-RAY DIFFRACTION95
2.44-2.540.26751710.20282702X-RAY DIFFRACTION95
2.54-2.650.23481500.20832835X-RAY DIFFRACTION98
2.65-2.790.22341450.20212844X-RAY DIFFRACTION99
2.79-2.970.2581440.20352859X-RAY DIFFRACTION99
2.97-3.20.20961620.18542861X-RAY DIFFRACTION99
3.2-3.520.24071480.17622848X-RAY DIFFRACTION98
3.52-4.030.20411690.16412908X-RAY DIFFRACTION100
4.03-5.070.19731640.15162873X-RAY DIFFRACTION98
5.07-42.50.22271680.19383016X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 20.2639 Å / Origin y: 0.2168 Å / Origin z: 7.2006 Å
111213212223313233
T0.1391 Å20.058 Å20.0034 Å2-0.062 Å2-0.0195 Å2--0.1026 Å2
L1.2623 °20.2929 °20.244 °2-0.1432 °20.1338 °2--0.427 °2
S-0.0503 Å °-0.0945 Å °0.0071 Å °0.0117 Å °0.0322 Å °-0.0016 Å °-0.071 Å °-0.021 Å °-0.0012 Å °
Refinement TLS groupSelection details: all

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