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- PDB-5t39: Crystal Structure of the N-terminal domain of EvdMO1 in the prese... -

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Basic information

Entry
Database: PDB / ID: 5t39
TitleCrystal Structure of the N-terminal domain of EvdMO1 in the presence of SAH and D-fucose
ComponentsEvdMO1
KeywordsTRANSFERASE / methyltransferase / Rossmann-like fold / SAM-dependent
Function / homology
Function and homology information


2-oxoglutarate-dependent dioxygenase activity / methyltransferase activity / methylation / iron ion binding
Similarity search - Function
Methyltransferase domain / Methyltransferase domain / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase domain-containing protein
Similarity search - Component
Biological speciesMicromonospora carbonacea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1004 Å
Model detailsResidues 1-233
AuthorsMcCulloch, K.M. / Starbird, C.A. / Chen, Q. / Perry, N.A. / Berndt, S. / Yamakawa, I. / Loukachevitch, L.V. / Iverson, T.M.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI106987 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)T32 HL007751 United States
American Heart Association12GRNT11920011 United States
American Heart Association14GRNT20390021 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10 RR026915 United States
CitationJournal: Biochemistry / Year: 2018
Title: The Structure of the Bifunctional Everninomicin Biosynthetic Enzyme EvdMO1 Suggests Independent Activity of the Fused Methyltransferase-Oxidase Domains.
Authors: Starbird, C.A. / Perry, N.A. / Chen, Q. / Berndt, S. / Yamakawa, I. / Loukachevitch, L.V. / Limbrick, E.M. / Bachmann, B.O. / Iverson, T.M. / McCulloch, K.M.
History
DepositionAug 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: EvdMO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7162
Polymers28,3321
Non-polymers3841
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.222, 41.270, 58.504
Angle α, β, γ (deg.)90.000, 98.580, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein EvdMO1


Mass: 28331.744 Da / Num. of mol.: 1 / Fragment: methyltransferase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora carbonacea (bacteria) / Gene: evdMO1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1C5AE13*PLUS
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.12 Å3/Da / Density % sol: 41.87 % / Mosaicity: 0.199 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 40% Tacsimate, pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 94601 / % possible obs: 98.5 % / Redundancy: 4.5 % / Biso Wilson estimate: 10.17 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.031 / Rrim(I) all: 0.068 / Χ2: 1.05 / Net I/av σ(I): 23.27 / Net I/σ(I): 9.2 / Num. measured all: 421834
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.1-1.123.70.4340.868195.3
1.12-1.144.10.380.918196.8
1.14-1.164.30.3390.936197.5
1.16-1.184.40.3050.952197.1
1.18-1.214.40.2730.958197.4
1.21-1.244.50.2530.963198.3
1.24-1.274.50.2310.967198.1
1.27-1.34.50.2040.974198.1
1.3-1.344.50.1880.975198.4
1.34-1.394.50.1710.976198.7
1.39-1.444.50.1470.982199
1.44-1.494.60.1160.989199.2
1.49-1.564.60.0950.991199.5
1.56-1.644.60.0880.993199.6
1.64-1.754.60.0810.993199.7
1.75-1.884.60.0710.994199.9
1.88-2.074.60.0560.9961100
2.07-2.374.60.0470.9971100
2.37-2.994.60.0440.9971100
2.99-504.30.0420.996196.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.1 Å22.47 Å
Translation1.1 Å22.47 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MGG

3mgg


Resolution: 1.1004→22.472 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 12.08
RfactorNum. reflection% reflection
Rfree0.1539 4666 4.93 %
Rwork0.137 --
obs0.1378 94581 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.86 Å2 / Biso mean: 14.5906 Å2 / Biso min: 7.01 Å2
Refinement stepCycle: final / Resolution: 1.1004→22.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1829 0 45 188 2062
Biso mean--10.43 23.62 -
Num. residues----233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061970
X-RAY DIFFRACTIONf_angle_d1.0092679
X-RAY DIFFRACTIONf_chiral_restr0.077287
X-RAY DIFFRACTIONf_plane_restr0.006358
X-RAY DIFFRACTIONf_dihedral_angle_d22.617745
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1004-1.11290.2061530.18122833298693
1.1129-1.1260.15921470.1622917306497
1.126-1.13970.16411650.13862916308197
1.1397-1.15410.14971800.13162902308297
1.1541-1.16930.14641590.13072942310197
1.1693-1.18530.12691570.12192947310497
1.1853-1.20230.13851580.11452954311298
1.2023-1.22020.13451480.11892966311497
1.2202-1.23930.12691410.11652961310298
1.2393-1.25960.1481530.11492975312898
1.2596-1.28130.12871660.1132978314498
1.2813-1.30460.13011600.11362965312598
1.3046-1.32970.12961430.11063006314998
1.3297-1.35680.14221550.11193021317699
1.3568-1.38630.15421480.1112970311898
1.3863-1.41860.13741520.10943018317099
1.4186-1.4540.12191410.11283005314699
1.454-1.49330.12441530.10673025317899
1.4933-1.53730.15331550.10373033318899
1.5373-1.58690.1311630.107330423205100
1.5869-1.64360.11411520.10830263178100
1.6436-1.70940.14291550.116430493204100
1.7094-1.78710.1221360.125830803216100
1.7871-1.88130.15041530.128930563209100
1.8813-1.99910.14021630.137230213184100
1.9991-2.15330.13841610.140530753236100
2.1533-2.36980.15621700.144330433213100
2.3698-2.71220.13951560.150330863242100
2.7122-3.41520.20781550.166431143269100
3.4152-22.47680.18161680.15852989315795

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