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- PDB-9l52: The ring expansion oxygenase SpoC in complex with Fe and stipital... -

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Basic information

Entry
Database: PDB / ID: 9l52
TitleThe ring expansion oxygenase SpoC in complex with Fe and stipitaldehyde
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: 1.8 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 ring expansion oxygenase SpoC in complex with Fe and stipitaldehyde
Authors: Liu, M. / He, X.
History
DepositionDec 23, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 7, 2026Provider: 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)83,3405
Polymers83,1932
Non-polymers1473
Water15,979887
1
A: ring expansion oxygenase SpoC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6883
Polymers41,5961
Non-polymers912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-13 kcal/mol
Surface area14380 Å2
MethodPISA
2
B: ring expansion oxygenase SpoC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6522
Polymers41,5961
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-13 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.584, 85.237, 104.423
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: 41596.277 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.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 887 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 43.63 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 24% (w/v) PEG 3350, 100 mM succinic acid

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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: 1.8→50 Å / Num. obs: 68189 / % possible obs: 99.8 % / Redundancy: 8.7 % / Biso Wilson estimate: 17.61 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.07 / Net I/σ(I): 9.5
Reflection shellResolution: 1.8→1.86 Å / Num. unique obs: 3337 / CC1/2: 0.276

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→43.98 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 24.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2567 3080 4.98 %
Rwork0.213 --
obs0.2152 61904 90.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→43.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4958 0 27 887 5872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035149
X-RAY DIFFRACTIONf_angle_d0.7866997
X-RAY DIFFRACTIONf_dihedral_angle_d5.167684
X-RAY DIFFRACTIONf_chiral_restr0.043747
X-RAY DIFFRACTIONf_plane_restr0.005915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.2992510.26641124X-RAY DIFFRACTION39
1.83-1.860.3283830.28751584X-RAY DIFFRACTION54
1.86-1.890.32291020.28131926X-RAY DIFFRACTION67
1.89-1.920.2925980.27622250X-RAY DIFFRACTION77
1.92-1.960.31311250.26862450X-RAY DIFFRACTION84
1.96-20.31741530.25262654X-RAY DIFFRACTION91
2-2.050.3061300.24462784X-RAY DIFFRACTION95
2.05-2.090.29261520.2452805X-RAY DIFFRACTION97
2.09-2.140.25051510.22992879X-RAY DIFFRACTION99
2.14-2.20.26221280.22492940X-RAY DIFFRACTION99
2.2-2.270.27681410.20962910X-RAY DIFFRACTION100
2.27-2.340.2951540.2192885X-RAY DIFFRACTION100
2.34-2.420.28721690.21842925X-RAY DIFFRACTION99
2.42-2.520.26631500.21722910X-RAY DIFFRACTION100
2.52-2.640.24641450.21542955X-RAY DIFFRACTION100
2.64-2.780.27031630.20662913X-RAY DIFFRACTION100
2.78-2.950.24921600.21552942X-RAY DIFFRACTION100
2.95-3.180.24511660.20012940X-RAY DIFFRACTION100
3.18-3.50.25391350.19532979X-RAY DIFFRACTION100
3.5-40.21221740.18122973X-RAY DIFFRACTION100
4-5.040.21341730.17842976X-RAY DIFFRACTION99
5.04-43.980.25331770.21623120X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -19.3069 Å / Origin y: -0.2606 Å / Origin z: 7.2591 Å
111213212223313233
T0.1307 Å20.006 Å20.0011 Å2-0.0679 Å2-0.0046 Å2--0.0986 Å2
L0.9372 °20.0272 °2-0.0532 °2-0.1896 °2-0.0543 °2--0.3426 °2
S-0.0223 Å °-0.0346 Å °-0.0568 Å °0.0032 Å °0.0064 Å °0.0028 Å °0.043 Å °0.0098 Å °0.0113 Å °
Refinement TLS groupSelection details: all

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