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- PDB-5ul2: Structure of Apo, SeMet-labeled Cobalamin-dependent S-adenosylmet... -

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Basic information

Entry
Database: PDB / ID: 5ul2
TitleStructure of Apo, SeMet-labeled Cobalamin-dependent S-adenosylmethionine radical enzyme OxsB
ComponentsOxsB protein
KeywordsMETAL BINDING PROTEIN / metalloprotein / cobalamin / radical SAM / S-adenosylmethionine / oxetanocin
Function / homology
Function and homology information


cobalamin binding / catalytic activity / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
OxsB-like / : / Radical SAM, alpha/beta horseshoe / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM
Similarity search - Domain/homology
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.552 Å
AuthorsBridwell-Rabb, J. / Drennan, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32-GM108189 United States
CitationJournal: Nature / Year: 2017
Title: A B12-dependent radical SAM enzyme involved in oxetanocin A biosynthesis.
Authors: Bridwell-Rabb, J. / Zhong, A. / Sun, H.G. / Drennan, C.L. / Liu, H.W.
History
DepositionJan 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OxsB protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,91118
Polymers87,8561
Non-polymers1,05517
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.392, 106.917, 117.494
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 OxsB protein


Mass: 87855.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: oxsB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star (DE3) / References: UniProt: O24770
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 3.42 Å3/Da / Density % sol: 64.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.1 M Bicine (pH 7.6), 10% w/v PEG 1500, 20% v/v ethylene glycol
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 39020 / % possible obs: 99.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 15.4
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3822 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SIRAS solved structure of apo-SeMet OxsB

Resolution: 2.552→39.539 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.58
RfactorNum. reflection% reflection
Rfree0.2278 2898 7.44 %
Rwork0.1866 --
obs0.1896 38972 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.552→39.539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5975 0 68 226 6269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026185
X-RAY DIFFRACTIONf_angle_d0.4648310
X-RAY DIFFRACTIONf_dihedral_angle_d12.5623780
X-RAY DIFFRACTIONf_chiral_restr0.04918
X-RAY DIFFRACTIONf_plane_restr0.0031052
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5518-2.59360.30891340.23961648X-RAY DIFFRACTION98
2.5936-2.63840.34351360.23711704X-RAY DIFFRACTION100
2.6384-2.68630.26821370.22981711X-RAY DIFFRACTION100
2.6863-2.7380.28971370.21261707X-RAY DIFFRACTION100
2.738-2.79390.26421360.20261695X-RAY DIFFRACTION100
2.7939-2.85460.25181380.18881722X-RAY DIFFRACTION100
2.8546-2.9210.23521360.19651687X-RAY DIFFRACTION100
2.921-2.9940.28031290.20851715X-RAY DIFFRACTION99
2.994-3.07490.24761460.19951679X-RAY DIFFRACTION98
3.0749-3.16540.28881310.20181718X-RAY DIFFRACTION99
3.1654-3.26750.25821400.20321701X-RAY DIFFRACTION100
3.2675-3.38420.28521370.19811735X-RAY DIFFRACTION100
3.3842-3.51960.22231320.18961724X-RAY DIFFRACTION100
3.5196-3.67970.24661440.17861731X-RAY DIFFRACTION100
3.6797-3.87350.21351420.18041700X-RAY DIFFRACTION99
3.8735-4.1160.19251370.16851704X-RAY DIFFRACTION97
4.116-4.43340.18971380.15551747X-RAY DIFFRACTION100
4.4334-4.87880.18341370.15441742X-RAY DIFFRACTION100
4.8788-5.58310.24021450.17891755X-RAY DIFFRACTION99
5.5831-7.02770.2211360.21451733X-RAY DIFFRACTION97
7.0277-39.54330.18851500.18861816X-RAY DIFFRACTION97

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