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- PDB-4xac: Crystal Structure of EvdO2 from Micromonospora carbonacea var. au... -

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Basic information

Entry
Database: PDB / ID: 4xac
TitleCrystal Structure of EvdO2 from Micromonospora carbonacea var. aurantiaca complexed with 2-oxoglutarate
ComponentsEvdO2
KeywordsOXIDOREDUCTASE / double stranded beta helix
Function / homology
Function and homology information


2-oxoglutarate-dependent dioxygenase activity / iron ion binding
Similarity search - Function
Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / q2cbj1_9rhob like domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / IMIDAZOLE / NICKEL (II) ION / EvdO2
Similarity search - Component
Biological speciesMicromonospora carbonacea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsMcCulloch, K.M. / McCranie, E.K. / Sarwar, M. / Mathieu, J.L. / Gitschlag, B.L. / Du, Y. / Bachmann, B.O. / Iverson, T.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Oxidative cyclizations in orthosomycin biosynthesis expand the known chemistry of an oxygenase superfamily.
Authors: McCulloch, K.M. / McCranie, E.K. / Smith, J.A. / Sarwar, M. / Mathieu, J.L. / Gitschlag, B.L. / Du, Y. / Bachmann, B.O. / Iverson, T.M.
History
DepositionDec 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Sep 30, 2015Group: Database references
Revision 1.3Aug 23, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: citation / diffrn_detector ...citation / diffrn_detector / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _diffrn_detector.type ..._citation.journal_id_CSD / _diffrn_detector.type / _pdbx_struct_oper_list.symmetry_operation / _software.version
Revision 1.4Sep 27, 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
A: EvdO2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8854
Polymers28,6111
Non-polymers2743
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.524, 65.372, 84.567
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein EvdO2


Mass: 28611.170 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora carbonacea (bacteria) / Variant: var. aurantiaca / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0M3KL01*PLUS
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.05 Å3/Da / Density % sol: 40.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 38% PEG 8000, 100 mM imidazole, 250 mM NaCl. Crystals soaked 30 min in 20 mM 2-oxoglutarate solution

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.127 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. obs: 19714 / % possible obs: 97.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 14
Reflection shellResolution: 1.87→1.94 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.324 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
HKL-2000data reduction
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XAB

4xab


Resolution: 1.87→37.99 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.209 1440 7.32 %
Rwork0.168 --
obs0.171 19681 96.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.18 Å2
Refinement stepCycle: LAST / Resolution: 1.87→37.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1933 0 16 128 2077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092103
X-RAY DIFFRACTIONf_angle_d1.112877
X-RAY DIFFRACTIONf_dihedral_angle_d15.172800
X-RAY DIFFRACTIONf_chiral_restr0.045289
X-RAY DIFFRACTIONf_plane_restr0.006388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.863-1.92950.22781350.1891726X-RAY DIFFRACTION93
1.9295-2.00680.21521450.1741823X-RAY DIFFRACTION99
2.0068-2.09810.22311440.17281842X-RAY DIFFRACTION99
2.0981-2.20870.21551410.16971824X-RAY DIFFRACTION99
2.2087-2.34710.22521490.16791845X-RAY DIFFRACTION98
2.3471-2.52830.2291420.17461830X-RAY DIFFRACTION98
2.5283-2.78260.23511430.18361839X-RAY DIFFRACTION98
2.7826-3.18510.2251470.17931827X-RAY DIFFRACTION97
3.1851-4.01220.21241430.15611838X-RAY DIFFRACTION95
4.0122-37.99920.17471510.16091847X-RAY DIFFRACTION92
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)
13.35420.16670.37583.1832-1.19973.32830.11290.2924-0.08340.00210.07090.19320.182-0.188-0.14810.16320.036-0.00530.1782-0.00130.186219.359134.191546.1854
23.26531.1205-1.80414.2823-2.91622.69520.2153-0.416-0.12290.187-0.5255-0.21810.12190.59880.09340.31980.0318-0.0150.28790.05220.347529.729319.80262.959
31.26370.04110.56851.23590.3890.4818-0.00990.1367-0.1302-0.061-0.0445-0.0056-0.03420.09810.06070.21330.05230.00360.24360.02350.192132.947933.376148.9885
42.50250.2166-0.09331.21830.01211.77060.048-0.2641-0.03270.1893-0.1057-0.0671-0.00040.18290.03720.1953-0.00010.00730.15640.04720.159832.64538.496656.9101
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 4:44)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 45:87)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 88:142)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 143:251)

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