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- PDB-6jzm: The intermediate forming O-C10 bond formation in AsqJ-catalyzed e... -

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Basic information

Entry
Database: PDB / ID: 6jzm
TitleThe intermediate forming O-C10 bond formation in AsqJ-catalyzed epoxidation
ComponentsIron/alpha-ketoglutarate-dependent dioxygenase asqJ
KeywordsOXIDOREDUCTASE / epoxidation / bonding
Function / homology
Function and homology information


(-)-cyclopenine synthase / dioxygenase activity / metal ion binding
Similarity search - Function
q2cbj1_9rhob like domain / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-CQ9 / : / SUCCINIC ACID / Iron/alpha-ketoglutarate-dependent dioxygenase asqJ
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsLiao, H.J. / Chan, N.L.
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: The intermediate forming O-C10 bond formation in AsqJ-catalyzed epoxidation
Authors: Liao, H.J. / Chan, N.L.
History
DepositionMay 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Iron/alpha-ketoglutarate-dependent dioxygenase asqJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4914
Polymers34,0231
Non-polymers4683
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area490 Å2
ΔGint-15 kcal/mol
Surface area13690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.147, 121.805, 66.617
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-582-

HOH

21B-623-

HOH

31B-717-

HOH

41B-727-

HOH

51B-729-

HOH

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Components

#1: Protein Iron/alpha-ketoglutarate-dependent dioxygenase asqJ / 4'-methoxyviridicatin/aspoquinolone biosynthesis cluster protein asqJ / Aspoquinolone biosynthesis protein J


Mass: 34022.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (mold)
Strain: FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139 / Gene: asqJ, AN9227 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5AR53, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Fe
#3: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#4: Chemical ChemComp-CQ9 / (3~{R},3'~{S})-4-methyl-3'-phenyl-spiro[1~{H}-1,4-benzodiazepine-3,2'-oxirane]-2,5-dione


Mass: 294.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14N2O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG 1000, Imidazole, calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→30 Å / Num. obs: 24830 / % possible obs: 99.7 % / Redundancy: 4 % / Net I/σ(I): 29.3
Reflection shellResolution: 1.88→1.95 Å / Num. unique obs: 2035

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→24.777 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 20.64
RfactorNum. reflection% reflection
Rfree0.2145 2019 8.6 %
Rwork0.1708 --
obs0.1746 23470 94.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.88→24.777 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2218 0 31 229 2478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082301
X-RAY DIFFRACTIONf_angle_d1.0873141
X-RAY DIFFRACTIONf_dihedral_angle_d8.2741888
X-RAY DIFFRACTIONf_chiral_restr0.066370
X-RAY DIFFRACTIONf_plane_restr0.007404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8801-1.92710.32031180.27911328X-RAY DIFFRACTION83
1.9271-1.97920.27781440.23421357X-RAY DIFFRACTION85
1.9792-2.03740.27361240.21191444X-RAY DIFFRACTION89
2.0374-2.10310.23471380.19231454X-RAY DIFFRACTION91
2.1031-2.17830.23521420.17461486X-RAY DIFFRACTION93
2.1783-2.26540.24671410.17491520X-RAY DIFFRACTION94
2.2654-2.36850.21821420.1731537X-RAY DIFFRACTION94
2.3685-2.49320.23481440.17461566X-RAY DIFFRACTION97
2.4932-2.64930.19871590.16961569X-RAY DIFFRACTION97
2.6493-2.85350.25351410.18491604X-RAY DIFFRACTION98
2.8535-3.14020.22011520.18791606X-RAY DIFFRACTION99
3.1402-3.59340.23231480.171634X-RAY DIFFRACTION99
3.5934-4.52280.17531590.13451638X-RAY DIFFRACTION99
4.5228-24.77930.16221670.14311708X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9441-0.47050.64452.20980.64060.9301-0.08520.3849-0.0737-0.3376-0.0819-0.64890.28220.8583-0.0310.18510.2120.15910.5582-0.00910.3025-10.8-27.4825-20.2376
23.2335-0.147-2.42112.1172-1.04652.47-0.20910.10980.74650.11160.0765-0.2802-0.63930.6141-0.2340.25-0.1589-0.13150.35070.04290.4975-11.9469-5.2691-8.3435
32.79390.9845-0.11683.21320.27196.6071-0.0174-0.88160.4150.7084-0.0994-0.0158-0.2017-0.09330.10720.36030.0112-0.04040.3597-0.06960.1967-26.2699-13.24263.4886
42.07691.8676-1.53874.7839-0.63872.8122-0.0384-0.01660.4501-0.1842-0.0803-0.102-0.67560.67940.060.1926-0.0862-0.06740.21540.06080.2448-19.1948-6.6219-16.2153
51.89530.2754-0.00542.52850.54151.1813-0.08570.32530.0426-0.1268-0.0243-0.2310.09590.370.04020.12360.01230.0310.17270.01740.0886-22.7922-19.5241-19.795
63.3389-0.10140.93740.6403-0.63821.53180.032-0.2025-0.28730.22990.0101-0.17540.05570.049-0.0630.19880.0318-0.01960.10170.01720.1289-25.7327-27.0048-8.5782
72.1441-0.3681.24842.0062-0.12212.69120.03450.0129-0.2170.28390.0606-0.50230.32530.3977-0.03680.1860.0703-0.02820.21970.02080.2175-14.449-27.1214-6.391
81.42760.4059-0.86122.7748-0.0241.7645-0.12180.1770.5256-0.1695-0.0162-0.0622-0.41010.19450.05070.1864-0.0352-0.05840.12090.05370.2153-29.1092-7.5425-19.0866
92.56340.1585-0.15521.3897-0.45331.6045-0.18910.71980.6041-0.3131-0.05760.0505-0.27220.29780.03610.2662-0.0469-0.05980.23220.11370.239-35.461-8.5441-27.9823
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 9 through 40 )
2X-RAY DIFFRACTION2chain 'B' and (resid 41 through 57 )
3X-RAY DIFFRACTION3chain 'B' and (resid 58 through 80 )
4X-RAY DIFFRACTION4chain 'B' and (resid 81 through 97 )
5X-RAY DIFFRACTION5chain 'B' and (resid 98 through 124 )
6X-RAY DIFFRACTION6chain 'B' and (resid 125 through 161 )
7X-RAY DIFFRACTION7chain 'B' and (resid 162 through 232 )
8X-RAY DIFFRACTION8chain 'B' and (resid 233 through 260 )
9X-RAY DIFFRACTION9chain 'B' and (resid 261 through 295 )

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