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- PDB-7eus: Crystal structures of 2-oxoglutarate dependent dioxygenase (CTB9)... -

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Basic information

Entry
Database: PDB / ID: 7eus
TitleCrystal structures of 2-oxoglutarate dependent dioxygenase (CTB9) from Cercospora sp. JNU001
Components2-oxoglutarate (2-OG)-dependent dioxygenase
KeywordsOXIDOREDUCTASE / 2-oxoglutarate-dependent dioxygenase / cercosporin
Function / homologyCOPPER (II) ION
Function and homology information
Biological speciesCercospora sojina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsHou, X.D. / Liu, X.Z. / Yuan, Z.B. / Rao, Y.J.
Funding support China, 4items
OrganizationGrant numberCountry
Other private2018YFA0901700 China
Other privateJUSRP12015 China
Other private2020M671329 China
Other private2020Z383 China
CitationJournal: Acs Catalysis / Year: 2022
Title: Molecular Basis of the Unusual Seven-Membered Methylenedioxy Bridge Formation Catalyzed by Fe(II)/alpha-KG-Dependent Oxygenase CTB9
Authors: Liu, X.Z. / Yuan, Z.B. / Su, H. / Hou, X.D. / Deng, Z.W. / Xu, H.B. / Guo, B.D. / Yin, D. / Sheng, X. / Rao, Y.J.
History
DepositionMay 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-oxoglutarate (2-OG)-dependent dioxygenase
B: 2-oxoglutarate (2-OG)-dependent dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2355
Polymers78,0162
Non-polymers2193
Water3,747208
1
A: 2-oxoglutarate (2-OG)-dependent dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1643
Polymers39,0081
Non-polymers1562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-0 kcal/mol
Surface area13570 Å2
MethodPISA
2
B: 2-oxoglutarate (2-OG)-dependent dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0722
Polymers39,0081
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.427, 147.916, 54.163
Angle α, β, γ (deg.)90.000, 105.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 2-oxoglutarate (2-OG)-dependent dioxygenase


Mass: 39008.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cercospora sojina (fungus) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 43.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 mM Bis-Tris pH 6.5, 3% (v/v) glycerol, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 28264 / % possible obs: 98.6 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.051 / Rrim(I) all: 0.135 / Χ2: 0.878 / Net I/σ(I): 6.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.385.80.35928050.8920.1610.3950.8898
2.38-2.486.40.32528120.9260.1380.3540.88798.1
2.48-2.596.30.28928030.9260.1240.3150.97998.1
2.59-2.736.90.25827910.9520.1050.2791.00498.2
2.73-2.96.90.19328220.9680.0790.2090.91198.7
2.9-3.126.50.16528240.9730.0690.1790.91498.5
3.12-3.446.90.13528320.9830.0550.1460.88598.9
3.44-3.936.90.11428450.9850.0460.1230.84999
3.93-4.956.80.128440.9870.0410.1080.7799
4.95-506.70.09828860.9850.040.1060.71898.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→42.62 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.798 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.407 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2197 2784 9.9 %RANDOM
Rwork0.1769 ---
obs0.1812 25304 97.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.7 Å2 / Biso mean: 28.651 Å2 / Biso min: 12.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0.1 Å2
2--0.52 Å20 Å2
3----0.37 Å2
Refinement stepCycle: final / Resolution: 2.3→42.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4761 0 8 208 4977
Biso mean--34.4 30.55 -
Num. residues----580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134895
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174380
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.6686646
X-RAY DIFFRACTIONr_angle_other_deg1.221.5810145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7625578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.820.962312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.13315760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2151550
X-RAY DIFFRACTIONr_chiral_restr0.0720.2606
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025525
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021129
LS refinement shellResolution: 2.291→2.351 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 172 -
Rwork0.206 1737 -
all-1909 -
obs--87.69 %

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