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

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Basic information

Entry
Database: PDB / ID: 4xab
TitleCrystal Structure of EvdO2 from Micromonospora carbonacea var. aurantiaca
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
IMIDAZOLE / NICKEL (II) ION / EvdO2
Similarity search - Component
Biological speciesMicromonospora carbonacea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 1.3Sep 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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 / _pdbx_struct_oper_list.symmetry_operation / _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)28,8084
Polymers28,6111
Non-polymers1973
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.612, 65.803, 84.462
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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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) / Strain: var. aurantiaca / Gene: evdO2 / 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.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.07 Å3/Da / Density % sol: 40.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 38% PEG8000, 100 mM imidazole, 250 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 24725 / % possible obs: 99.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 20.21 Å2 / Rmerge(I) obs: 0.068 / Χ2: 1.143 / Net I/av σ(I): 18.142 / Net I/σ(I): 13.1 / Num. measured all: 89257
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.75-1.813.60.29624040.92699.6
1.81-1.893.60.22824451.038100
1.89-1.973.60.16924241.142100
1.97-2.073.60.1324451.245100
2.07-2.23.60.11224491.336100
2.2-2.383.60.124601.222100
2.38-2.613.60.0824641.3100
2.61-2.993.60.06824781.147100
2.99-3.773.60.05825071.122100
3.77-503.40.0526490.94399.4

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OBZ

3obz


Resolution: 1.75→38.044 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2037 1805 7.32 %
Rwork0.1743 22863 -
obs0.1765 24668 99.75 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.34 Å2 / Biso mean: 28.5928 Å2 / Biso min: 10.25 Å2
Refinement stepCycle: final / Resolution: 1.75→38.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1982 0 11 171 2164
Biso mean--28.66 36.16 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072091
X-RAY DIFFRACTIONf_angle_d1.0572863
X-RAY DIFFRACTIONf_chiral_restr0.043291
X-RAY DIFFRACTIONf_plane_restr0.006384
X-RAY DIFFRACTIONf_dihedral_angle_d12.594785
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7482-1.79540.2621350.19761712184798
1.7954-1.84830.25951360.201717281864100
1.8483-1.90790.23041340.186317091843100
1.9079-1.97610.22991380.179417391877100
1.9761-2.05520.2241380.171317521890100
2.0552-2.14870.23911370.172217311868100
2.1487-2.2620.21581380.16817481886100
2.262-2.40370.18021380.170117481886100
2.4037-2.58930.22661390.1817511890100
2.5893-2.84980.24121400.185817721912100
2.8498-3.26190.18841410.186318001941100
3.2619-4.10890.18991410.162217831924100
4.1089-38.05340.17241500.16651890204099
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)
12.76390.12340.77253.5258-1.36763.5668-0.01470.1307-0.1497-0.14960.0640.2120.1846-0.2217-0.030.09930.03070.02350.1475-0.00980.159719.021835.059845.7576
21.83580.4818-1.62941.9618-2.31055.04520.1362-0.3165-0.1715-0.0167-0.3549-0.24540.36670.77950.0790.31190.0390.03470.30540.06890.407329.745119.723162.3466
31.90370.00510.55321.29130.53620.4247-0.02110.2118-0.1293-0.0957-0.0175-0.02020.0240.15510.05860.15850.02990.0140.13380.02380.129632.848133.594448.8306
41.94860.18470.25081.18110.14151.34910.0127-0.2216-0.02460.1272-0.0748-0.08250.00630.1520.0530.15320.00570.00610.13370.04380.118332.622538.701356.8746
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 3:43)A3 - 43
2X-RAY DIFFRACTION2(chain A and resid 44:87)A44 - 87
3X-RAY DIFFRACTION3(chain A and resid 88:142)A88 - 142
4X-RAY DIFFRACTION4(chain A and resid 143:251)A143 - 251

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