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- PDB-5t38: Crystal Structure of the N-terminal domain of EvdMO1 with SAH bound -

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Basic information

Entry
Database: PDB / ID: 5t38
TitleCrystal Structure of the N-terminal domain of EvdMO1 with SAH bound
ComponentsEvdMO1
KeywordsTRANSFERASE / methyltransferase / Rossmann-like fold / SAM-dependent
Function / homologyMethyltransferase domain / Methyltransferase domain / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase domain-containing protein
Function and homology information
Biological speciesMicromonospora carbonacea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1502 Å
Model detailsResidues 1-233
AuthorsMcCulloch, K.M. / Berndt, S. / Yamakawa, I. / Chen, Q. / Loukachevitch, L.V. / Starbird, C. / Perry, N.A. / 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

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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
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.427, 41.272, 56.465
Angle α, β, γ (deg.)90.000, 99.800, 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 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.08 Å3/Da / Density % sol: 40.98 % / Mosaicity: 0.247 °
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: Apr 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 79855 / % possible obs: 96.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.052 / Net I/av σ(I): 20.222 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.15-1.172.30.3470.836170
1.17-1.192.50.3480.867185.9
1.19-1.213.20.3270.901194.3
1.21-1.243.40.3160.925195.6
1.24-1.273.50.290.932197.1
1.27-1.33.60.2660.945197.8
1.3-1.333.60.2330.954198.2
1.33-1.363.60.2050.965198.3
1.36-1.43.60.1730.974198.5
1.4-1.453.60.1450.979198.5
1.45-1.53.60.1180.985199.1
1.5-1.563.60.0970.99199.2
1.56-1.633.60.0820.992199.2
1.63-1.723.60.0730.993199.4
1.72-1.833.70.0690.992199.6
1.83-1.973.70.0720.991199.8
1.97-2.163.70.0680.9921100
2.16-2.483.70.0550.9941100
2.48-3.123.70.0340.9981100
3.12-503.50.0290.998195.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MGG
Resolution: 1.1502→32.002 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.51
RfactorNum. reflection% reflection
Rfree0.1682 3896 4.88 %
Rwork0.1529 --
obs0.1536 79826 96.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.55 Å2 / Biso mean: 17.7878 Å2 / Biso min: 6.75 Å2
Refinement stepCycle: final / Resolution: 1.1502→32.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1869 0 45 322 2236
Biso mean--10.67 30.48 -
Num. residues----238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062002
X-RAY DIFFRACTIONf_angle_d0.9842728
X-RAY DIFFRACTIONf_chiral_restr0.072295
X-RAY DIFFRACTIONf_plane_restr0.006363
X-RAY DIFFRACTIONf_dihedral_angle_d21.399757
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1502-1.16420.2091100.22511844195466
1.1642-1.17890.2361270.22622218234578
1.1789-1.19450.24151210.22522465258689
1.1945-1.21080.22781210.20712640276194
1.2108-1.22810.23821440.21542689283395
1.2281-1.24650.24061370.2082697283496
1.2465-1.26590.22291440.19072713285797
1.2659-1.28670.19641490.18842728287797
1.2867-1.30890.17071300.17812727285798
1.3089-1.33270.16361440.1712787293198
1.3327-1.35830.18841460.17462715286198
1.3583-1.3860.18711320.1672772290498
1.386-1.41620.18061390.16162786292599
1.4162-1.44910.18111360.16092799293599
1.4491-1.48540.17761320.15622786291899
1.4854-1.52550.15981460.1532790293699
1.5255-1.57040.15181500.14152777292799
1.5704-1.62110.14911390.13982804294399
1.6211-1.6790.16371360.137227962932100
1.679-1.74630.15251410.146228052946100
1.7463-1.82570.16691240.1452833295799
1.8257-1.9220.14981540.141228102964100
1.922-2.04240.15111390.141328332972100
2.0424-2.20.1371560.135428382994100
2.2-2.42130.14141600.135528182978100
2.4213-2.77160.17941340.146428542988100
2.7716-3.49120.17741490.15128623011100
3.4912-32.0140.1671560.14812744290094
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.88153.0519-0.81056.0127-0.9651.01170.0423-0.0588-0.02890.243-0.0607-0.1856-0.00120.14420.00950.07070.01160.00190.1297-0.00370.089770.21699.994860.7066
21.3317-0.35810.44670.29130.09680.4054-0.07520.1885-0.19330.09960.04760.0887-0.0467-0.20760.02160.16120.01580.03810.17730.00780.174557.04153.952155.8335
31.7011-1.3187-0.70782.58620.58831.4560.09740.09620.1524-0.1899-0.0659-0.1833-0.10720.037-0.01680.0707-0.00280.00940.06940.0090.084250.15715.586668.7056
42.48781.0954-1.55632.35250.93672.92030.033-0.11330.0622-0.0278-0.0058-0.0887-0.03070.1381-0.00190.04960.0096-0.0120.10560.00920.094660.86879.946472.0532
50.680.2154-0.07781.92130.26770.9279-0.0128-0.0556-0.00190.01750.0018-0.02690.0794-0.00180.01060.06040.0025-0.00140.08350.00150.060544.23084.03176.5395
60.76910.3315-0.18241.2773-0.18230.3385-0.06120.036-0.0703-0.1860.0440.08970.0555-0.07970.01790.118-0.0115-0.0190.103-0.00240.068737.527-1.207569.5303
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 24 )A-4 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 40 )A25 - 40
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 74 )A41 - 74
4X-RAY DIFFRACTION4chain 'A' and (resid 75 through 109 )A75 - 109
5X-RAY DIFFRACTION5chain 'A' and (resid 110 through 159 )A110 - 159
6X-RAY DIFFRACTION6chain 'A' and (resid 160 through 233 )A160 - 233

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