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- PDB-5m0t: Alpha-ketoglutarate-dependent non-heme iron oxygenase EasH -

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Basic information

Entry
Database: PDB / ID: 5m0t
TitleAlpha-ketoglutarate-dependent non-heme iron oxygenase EasH
ComponentsAlpha-ketoglutarate-dependent non-heme iron oxygenase EasH
KeywordsOXIDOREDUCTASE / cycloclavine biosynthesis / EasH / Alpha-ketoglutarate-dependent non-heme iron oxygenase / ergot alkaloids
Function / homology
Function and homology information


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 / : / Alpha-ketoglutarate-dependent non-heme iron oxygenase EasH
Similarity search - Component
Biological speciesAspergillus japonicus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJakubczyk, D. / Caputi, L. / Stevenson, C.E.M. / Lawson, D.M. / O'Connor, S.E.
CitationJournal: Chem. Commun. (Camb.) / Year: 2016
Title: Structural characterization of EasH (Aspergillus japonicus) - an oxidase involved in cycloclavine biosynthesis.
Authors: Jakubczyk, D. / Caputi, L. / Stevenson, C.E. / Lawson, D.M. / O'Connor, S.E.
History
DepositionOct 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Jan 17, 2024Group: 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 / struct_ncs_dom_lim
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_alt_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-ketoglutarate-dependent non-heme iron oxygenase EasH
B: Alpha-ketoglutarate-dependent non-heme iron oxygenase EasH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,98811
Polymers65,1762
Non-polymers8129
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-143 kcal/mol
Surface area21210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.250, 100.170, 148.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: 9 - 286 / Label seq-ID: 10 - 287

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Alpha-ketoglutarate-dependent non-heme iron oxygenase EasH


Mass: 32587.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The sequence is not currently in any publically accessible database
Source: (gene. exp.) Aspergillus japonicus (mold) / Plasmid: pOPIN-J / Production host: Escherichia coli (E. coli) / Variant (production host): SOLUBL21 / References: UniProt: A0A1L1QK38*PLUS
#2: Chemical ChemComp-FE2 / FE (II) ION


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


Mass: 146.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.3 Å3/Da / Density % sol: 46.58 % / Description: NULL
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: NULL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→47.47 Å / Num. obs: 31397 / % possible obs: 99.7 % / Redundancy: 5.9 % / Biso Wilson estimate: 34.6 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.151 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.2-2.265.71.4131.30.539199.5
9.84-47.474.80.0350.999199

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Processing

Software
NameVersionClassification
Aimless0.5.7data scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.2data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NAO

4nao


Resolution: 2.2→47.47 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.947 / SU B: 17.557 / SU ML: 0.208 / SU R Cruickshank DPI: 0.3046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.305 / ESU R Free: 0.213
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 1521 4.8 %RANDOM
Rwork0.2178 ---
obs0.2191 29876 99.62 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 137.17 Å2 / Biso mean: 50.114 Å2 / Biso min: 10.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2--0.56 Å20 Å2
3----0.29 Å2
Refinement stepCycle: final / Resolution: 2.2→47.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4383 0 36 110 4529
Biso mean--51.98 40.96 -
Num. residues----566
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194566
X-RAY DIFFRACTIONr_bond_other_d0.0020.024254
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.9656166
X-RAY DIFFRACTIONr_angle_other_deg0.94239781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2185570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59524.07199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79415742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1021529
X-RAY DIFFRACTIONr_chiral_restr0.0780.2680
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215187
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021022
X-RAY DIFFRACTIONr_mcbond_it1.5671.4472277
X-RAY DIFFRACTIONr_mcbond_other1.5651.4472276
X-RAY DIFFRACTIONr_mcangle_it2.3962.1642848
Refine LS restraints NCS

Ens-ID: 1 / Number: 18106 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 124 -
Rwork0.357 2173 -
all-2297 -
obs--99.44 %
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)
13.6842-0.2809-1.94083.50860.50734.16130.2846-0.38850.42480.21120.2097-0.086-0.06680.3936-0.49430.0437-0.0378-0.00040.3596-0.12430.347250.3032.9286196.4416
20.41322.01390.054510.04850.26910.0235-0.12530.0181-0.0535-0.78160.2682-0.42090.0053-0.003-0.14290.48340.03130.04250.7689-0.05110.924728.548410.015185.3577
31.70730.4228-2.18040.7455-0.42464.7790.3808-0.04680.77790.09030.2856-0.0092-0.36920.1547-0.66640.1284-0.03170.09980.2796-0.12470.696946.544110.125186.6846
41.30410.1889-1.26671.4847-0.38533.3770.207-0.04530.5213-0.05420.23580.1403-0.0444-0.037-0.44280.061-0.00090.01010.228-0.07050.529544.00175.2991184.6416
54.71240.0591-1.05233.721-1.12613.91590.29180.52860.16-0.3389-0.0705-0.03010.0231-0.5672-0.22120.05010.03430.00210.54910.13670.310535.4615-1.0453144.5189
60.25120.27040.49810.39471.20575.46080.40460.17820.14070.2210.29940.0532-0.53730.9415-0.7041.04060.0140.40390.59420.16781.045454.388614.026152.5027
72.5942-1.23021.33421.55760.15484.59730.2850.30940.6306-0.3650.1091-0.2823-0.46070.0712-0.39410.26830.05240.17920.43070.21180.724646.299913.4682153.0848
81.4904-0.258-1.38280.86240.80033.72910.21320.23990.46980.00840.1052-0.2303-0.0609-0.2442-0.31840.05240.01540.00680.31190.15930.459943.60883.524156.2398
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 53
2X-RAY DIFFRACTION2A54 - 73
3X-RAY DIFFRACTION3A74 - 125
4X-RAY DIFFRACTION4A126 - 293
5X-RAY DIFFRACTION5B9 - 45
6X-RAY DIFFRACTION6B46 - 66
7X-RAY DIFFRACTION7B67 - 94
8X-RAY DIFFRACTION8B95 - 287

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