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

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Basic information

Entry
Database: PDB / ID: 7euu
TitleCrystal structures of 2-oxoglutarate dependent dioxygenase (CTB9) in complex with N-oxalylglycine and pre-cercosporin
Components2-oxoglutarate (2-OG)-dependent dioxygenase
KeywordsOXIDOREDUCTASE / 2-oxoglutarate-dependent dioxygenase / cercosporin
Function / homologyCOPPER (II) ION / Chem-JD9 / N-OXALYLGLYCINE
Function and homology information
Biological speciesCercospora sojina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.202 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 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)78,79110
Polymers77,1722
Non-polymers1,6188
Water4,324240
1
A: 2-oxoglutarate (2-OG)-dependent dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3334
Polymers38,5861
Non-polymers7473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-7 kcal/mol
Surface area13230 Å2
MethodPISA
2
B: 2-oxoglutarate (2-OG)-dependent dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4576
Polymers38,5861
Non-polymers8715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-7 kcal/mol
Surface area13340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.027, 97.901, 153.045
Angle α, β, γ (deg.)90.000, 94.040, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-569-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 38586.039 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)

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Non-polymers , 5 types, 248 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#4: Chemical ChemComp-JD9 / 2,6,11-trimethoxy-4,7,9-tris(oxidanyl)-1,12-bis[(2R)-2-oxidanylpropyl]perylene-3,10-dione


Mass: 536.527 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H28O10 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
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: BL18U / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 30959 / % possible obs: 98.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.024 / Rrim(I) all: 0.063 / Χ2: 0.941 / Net I/σ(I): 9.3 / Num. measured all: 207362
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.246.30.28315060.9610.1210.3090.96698.4
2.24-2.286.20.2515380.9740.1080.2730.97998.4
2.28-2.326.30.22715370.9770.0970.2470.9796.1
2.32-2.3770.21214700.980.0860.2290.99898.1
2.37-2.426.80.19516040.9820.0790.210.99599.3
2.42-2.486.90.16414890.9890.0670.1771.02397.1
2.48-2.546.70.14615480.9910.060.1581.018100
2.54-2.616.70.12915390.9920.0530.1390.9998.6
2.61-2.696.60.12315470.990.0510.1341.04298.2
2.69-2.776.30.10115600.9930.0440.1110.97599.4
2.77-2.876.60.08515140.9940.0360.0931.01498.6
2.87-2.996.90.07915800.9950.0320.0850.99699.3
2.99-3.1270.07315300.9950.0290.0780.97899
3.12-3.296.90.06415590.9960.0260.0690.97199.3
3.29-3.496.80.05715790.9960.0240.0620.93699.4
3.49-3.766.60.05215540.9960.0220.0560.88599.7
3.76-4.147.20.0515650.9980.020.0540.88599.6
4.14-4.7470.04715550.9970.0190.050.84999.5
4.74-5.976.50.04315870.9970.0180.0470.71199.7
5.97-506.70.04215980.9970.0180.0460.6799.5

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EUS

7eus


Resolution: 2.202→25.444 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2456 3090 10.05 %
Rwork0.2072 27652 -
obs0.211 30742 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.4 Å2 / Biso mean: 34.4147 Å2 / Biso min: 9.02 Å2
Refinement stepCycle: final / Resolution: 2.202→25.444 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4732 0 108 240 5080
Biso mean--33.33 34.86 -
Num. residues----576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074985
X-RAY DIFFRACTIONf_angle_d0.7626764
X-RAY DIFFRACTIONf_chiral_restr0.044686
X-RAY DIFFRACTIONf_plane_restr0.005882
X-RAY DIFFRACTIONf_dihedral_angle_d9.8662956
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.202-2.2360.28731250.2518114790
2.236-2.27270.31021240.2549124196
2.2727-2.31180.36151700.2705119296
2.3118-2.35390.31421270.2614122595
2.3539-2.39910.31241600.2812121199
2.3991-2.4480.3191550.2596124998
2.448-2.50120.34211440.2601122398
2.5012-2.55930.30311530.24761284100
2.5593-2.62330.291450.2511123797
2.6233-2.69410.30821070.2443129299
2.6941-2.77330.28771420.2416128499
2.7733-2.86270.28641340.219125198
2.8627-2.96490.28861480.22691303100
2.9649-3.08340.27591200.2344124198
3.0834-3.22350.27241460.22271287100
3.2235-3.39310.27021340.20641263100
3.3931-3.60510.20511340.1924129499
3.6051-3.88250.22651370.18431265100
3.8825-4.27160.20981600.1715127099
4.2716-4.88590.17921490.15531293100

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