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- PDB-6k0f: The crystal structure of cyclopenin-bound AsqJ quinary complex -

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Basic information

Entry
Database: PDB / ID: 6k0f
TitleThe crystal structure of cyclopenin-bound AsqJ quinary complex
ComponentsIron/alpha-ketoglutarate-dependent dioxygenase asqJ
KeywordsOXIDOREDUCTASE / cyclopenin / dioxygen / product / 2OG
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
2-OXOGLUTARIC ACID / Chem-CQ9 / : / HYDROGEN PEROXIDE / Iron/alpha-ketoglutarate-dependent dioxygenase asqJ
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.634 Å
AuthorsLiao, H.J. / Chan, N.L.
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: The crystal structure of cyclopenin-bound AsqJ quinary complex
Authors: Liao, H.J. / Chan, N.L.
History
DepositionMay 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)36,6385
Polymers36,1071
Non-polymers5304
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-9 kcal/mol
Surface area13970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.839, 120.943, 66.722
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-587-

HOH

21B-644-

HOH

31B-696-

HOH

41B-720-

HOH

51B-724-

HOH

61B-726-

HOH

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Components

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Protein , 1 types, 1 molecules B

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


Mass: 36107.246 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

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Non-polymers , 5 types, 230 molecules

#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#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: Chemical ChemComp-PEO / HYDROGEN PEROXIDE / Hydrogen peroxide


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.06 Å3/Da / Density % sol: 40.37 %
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: Jun 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→30 Å / Num. obs: 37248 / % possible obs: 99.7 % / Redundancy: 4 % / Biso Wilson estimate: 22.23 Å2 / CC1/2: 0.839 / Net I/σ(I): 29.2
Reflection shellResolution: 1.63→1.69 Å / Num. unique obs: 3627 / CC1/2: 0.839 / Rpim(I) all: 0.27 / Rrim(I) all: 0.54

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5y7r

5y7r


Resolution: 1.634→29.211 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.96
RfactorNum. reflection% reflection
Rfree0.1954 1863 5 %
Rwork0.1756 --
obs0.1766 37228 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.44 Å2 / Biso mean: 29.1006 Å2 / Biso min: 12.31 Å2
Refinement stepCycle: final / Resolution: 1.634→29.211 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2227 0 55 226 2508
Biso mean--34.68 34.24 -
Num. residues----288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072311
X-RAY DIFFRACTIONf_angle_d1.0733158
X-RAY DIFFRACTIONf_chiral_restr0.072371
X-RAY DIFFRACTIONf_plane_restr0.009404
X-RAY DIFFRACTIONf_dihedral_angle_d8.5391900
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.634-1.67790.26691510.225263697
1.6779-1.72730.23421570.20372677100
1.7273-1.7830.21421260.19652706100
1.783-1.84670.2091320.19232709100
1.8467-1.92070.21791490.192696100
1.9207-2.0080.21251450.17672709100
2.008-2.11390.19991550.18032681100
2.1139-2.24630.20331290.17432726100
2.2463-2.41960.18811680.18052710100
2.4196-2.6630.22511280.18892746100
2.663-3.0480.20841110.19482780100
3.048-3.83880.20161470.1744276099
3.8388-29.2110.15931650.1472282998
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)
14.4174-0.49921.34194.79321.5572.1292-0.05350.2145-0.1557-0.25380.1053-0.46140.29020.4505-0.03950.2150.1060.06630.3097-0.01460.2449-10.555-27.7149-19.778
27.3631-1.9939-6.60854.75022.58128.5353-0.0599-0.28670.6675-0.0460.2151-0.4291-0.69720.7734-0.22990.2335-0.0855-0.08570.2606-0.01730.3647-11.8085-5.1063-8.3449
31.8480.39820.6671.44480.03691.417-0.0099-0.13710.09180.132-0.011-0.1211-0.02260.11420.01950.15220.0291-0.00260.1294-0.01150.1522-23.7379-17.0967-9.3561
45.8118-0.5446-0.51130.3518-0.59791.435-0.0065-0.0842-0.5638-0.0579-0.0223-0.10080.23110.06490.01520.21490.05830.01570.13260.02660.196-24.8829-27.6527-16.1498
51.9964-1.80090.99863.0979-1.57434.27280.2102-0.1938-0.46470.2815-0.0135-0.23150.67980.0758-0.19860.24420.1037-0.01260.20650.00430.2557-15.2862-32.4974-5.496
61.3440.17070.472.05410.06551.3593-0.0228-0.0745-0.10140.16760.0642-0.47450.12660.314-0.05070.15450.0567-0.01490.214-0.00140.2178-13.6918-22.7408-7.0371
72.02491.0867-0.83322.3797-0.34793.7598-0.04450.06340.4374-0.09590.02020.0026-0.36250.150.00940.16910.0085-0.03440.10830.02910.2114-28.9732-7.2895-19.071
86.05270.48511.88042.2632-0.30423.6821-0.05280.48710.0823-0.27920.00550.06890.0645-0.01680.0450.17610.00170.01580.14060.02520.1095-37.5603-14.3479-27.607
93.84742.08880.18635.9668-0.38732.6751-0.46360.59951.6979-0.14910.25450.6308-0.59910.29760.14780.3582-0.0679-0.04960.29350.16650.434-31.9953-0.8458-27.8437
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 8 through 40 )B8 - 40
2X-RAY DIFFRACTION2chain 'B' and (resid 41 through 57 )B41 - 57
3X-RAY DIFFRACTION3chain 'B' and (resid 58 through 146 )B58 - 146
4X-RAY DIFFRACTION4chain 'B' and (resid 147 through 161 )B147 - 161
5X-RAY DIFFRACTION5chain 'B' and (resid 162 through 191 )B162 - 191
6X-RAY DIFFRACTION6chain 'B' and (resid 192 through 232 )B192 - 232
7X-RAY DIFFRACTION7chain 'B' and (resid 233 through 259 )B233 - 259
8X-RAY DIFFRACTION8chain 'B' and (resid 260 through 279 )B260 - 279
9X-RAY DIFFRACTION9chain 'B' and (resid 280 through 295 )B280 - 295

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