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

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Basic information

Entry
Database: PDB / ID: 7eut
TitleCrystal structures of 2-oxoglutarate dependent dioxygenase (CTB9) in complex with N-oxalylglycine
Components2-oxoglutarate (2-OG)-dependent dioxygenase
KeywordsOXIDOREDUCTASE / 2-oxoglutarate-dependent dioxygenase / cercosporin
Function / homologyCOPPER (II) ION / N-OXALYLGLYCINE
Function and homology information
Biological speciesCercospora sojina (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.497 Å
AuthorsHou, X.D. / Liu, X.Z. / Yuan, Z.B. / Yin, D.J. / 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)77,7488
Polymers77,1722
Non-polymers5756
Water5,729318
1
A: 2-oxoglutarate (2-OG)-dependent dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7973
Polymers38,5861
Non-polymers2112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-9 kcal/mol
Surface area13700 Å2
MethodPISA
2
B: 2-oxoglutarate (2-OG)-dependent dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9515
Polymers38,5861
Non-polymers3654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-8 kcal/mol
Surface area13450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.958, 100.945, 154.506
Angle α, β, γ (deg.)90.000, 93.720, 90.000
Int Tables number5
Space group name H-MC121

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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, 324 molecules

#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-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
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: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.542 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Sep 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.497→23.98 Å / Num. obs: 22882 / % possible obs: 99.67 % / Redundancy: 7.62 % / Rsym value: 0.226 / Net I/av σ(I): 10.71 / Net I/σ(I): 5.531
Reflection shell
Resolution (Å)Num. unique obsRsym valueDiffraction-ID
2.497-2.58622110.4961
2.586-2.68922920.4611
2.689-2.81222940.3811
2.812-2.9622560.3261
2.96-3.14522950.2891
3.145-3.38722930.2481
3.387-3.72723040.2131
3.727-4.26323050.1991
4.263-5.36122990.1941

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
SAINTV8.38Adata scaling
PDB_EXTRACT3.27data extraction
PROTEUM PLUSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EUS

7eus


Resolution: 2.497→23.623 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2377 2236 9.8 %
Rwork0.1878 20581 -
obs0.1927 22817 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.32 Å2 / Biso mean: 30.1408 Å2 / Biso min: 14.71 Å2
Refinement stepCycle: final / Resolution: 2.497→23.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4732 0 32 318 5082
Biso mean--24.23 32.86 -
Num. residues----576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044901
X-RAY DIFFRACTIONf_angle_d0.6376633
X-RAY DIFFRACTIONf_chiral_restr0.042682
X-RAY DIFFRACTIONf_plane_restr0.004878
X-RAY DIFFRACTIONf_dihedral_angle_d8.0482915
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.497-2.54710.34721190.2586115391
2.5471-2.60630.30421280.26131290100
2.6063-2.67140.31371460.23081300100
2.6714-2.74350.27081530.23731286100
2.7435-2.82410.29411430.22131272100
2.8241-2.91510.24911550.21241274100
2.9151-3.01910.2311370.21411298100
3.0191-3.13970.28091370.21341282100
3.1397-3.28230.26451600.21241285100
3.2823-3.45480.24361510.18731273100
3.4548-3.67050.20681460.17271305100
3.6705-3.95270.20021350.1681301100
3.9527-4.34830.21521370.15411298100
4.3483-4.97240.19651210.13981321100
4.9724-6.24550.21741400.17471312100

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