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- PDB-6ec3: Crystal Structure of EvdMO1 -

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Basic information

Entry
Database: PDB / ID: 6ec3
TitleCrystal Structure of EvdMO1
ComponentsMethyltransferase domain-containing protein
KeywordsTRANSFERASE / oxidoreductase / methyltransferase / Rossmann-like fold / SAM-dependent / nonheme iron AKG-dependent oxygenase
Function / homology
Function and homology information


phytanoyl-CoA dioxygenase activity / methyltransferase activity / methylation
Similarity search - Function
Methyltransferase domain / Methyltransferase domain / q2cbj1_9rhob like domain / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / Jelly Rolls / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Methyltransferase domain-containing protein
Similarity search - Component
Biological speciesMicromonospora carbonacea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
Model detailsfull-length
AuthorsMcCulloch, K.M. / Iverson, T.M. / Starbird, C.A. / Perry, N.A. / Chen, Q. / Berndt, S. / Yamakawa, I. / Loukachevitch, L.V.
Funding support United States, 5items
OrganizationGrant numberCountry
American Heart Association12GRNT11920011 United States
American Heart Association14GRNT20390021 United States
American Heart Association16PRE30180007 United States
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)T32HL007751 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 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyltransferase domain-containing protein
B: Methyltransferase domain-containing protein
C: Methyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,0909
Polymers156,2863
Non-polymers8046
Water00
1
A: Methyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3633
Polymers52,0951
Non-polymers2682
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3633
Polymers52,0951
Non-polymers2682
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Methyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3633
Polymers52,0951
Non-polymers2682
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)191.633, 191.633, 269.618
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq -13:-7 or resseq 1:29 or resseq...
21(chain B and (resseq -13:-7 or resseq 1:29 or resseq...
31(chain C and (resseq -13:-7 or resseq 1:29 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq -13:-7 or resseq 1:29 or resseq...A-13 - -7
121(chain A and (resseq -13:-7 or resseq 1:29 or resseq...A1 - 29
131(chain A and (resseq -13:-7 or resseq 1:29 or resseq...A40 - 120
141(chain A and (resseq -13:-7 or resseq 1:29 or resseq...A122 - 148
151(chain A and (resseq -13:-7 or resseq 1:29 or resseq...A150 - 160
161(chain A and (resseq -13:-7 or resseq 1:29 or resseq...A164
171(chain A and (resseq -13:-7 or resseq 1:29 or resseq...A166 - 172
181(chain A and (resseq -13:-7 or resseq 1:29 or resseq...A195 - 210
191(chain A and (resseq -13:-7 or resseq 1:29 or resseq...A240 - 285
1101(chain A and (resseq -13:-7 or resseq 1:29 or resseq...A288 - 430
1111(chain A and (resseq -13:-7 or resseq 1:29 or resseq...A432 - 442
1121(chain A and (resseq -13:-7 or resseq 1:29 or resseq...A500 - 501
211(chain B and (resseq -13:-7 or resseq 1:29 or resseq...B-13 - -7
221(chain B and (resseq -13:-7 or resseq 1:29 or resseq...B1 - 29
231(chain B and (resseq -13:-7 or resseq 1:29 or resseq...B-13 - 148
241(chain B and (resseq -13:-7 or resseq 1:29 or resseq...B0
251(chain B and (resseq -13:-7 or resseq 1:29 or resseq...B166 - 1772
261(chain B and (resseq -13:-7 or resseq 1:29 or resseq...B212 - 217
271(chain B and (resseq -13:-7 or resseq 1:29 or resseq...B-13 - 442
281(chain B and (resseq -13:-7 or resseq 1:29 or resseq...B212 - 217
291(chain B and (resseq -13:-7 or resseq 1:29 or resseq...B219 - 285
2101(chain B and (resseq -13:-7 or resseq 1:29 or resseq...B288 - 430
2111(chain B and (resseq -13:-7 or resseq 1:29 or resseq...B432 - 442
2121(chain B and (resseq -13:-7 or resseq 1:29 or resseq...B500 - 501
311(chain C and (resseq -13:-7 or resseq 1:29 or resseq...C-13 - -7
321(chain C and (resseq -13:-7 or resseq 1:29 or resseq...C1 - 29
331(chain C and (resseq -13:-7 or resseq 1:29 or resseq...C-13 - 148
341(chain C and (resseq -13:-7 or resseq 1:29 or resseq...C0
351(chain C and (resseq -13:-7 or resseq 1:29 or resseq...C166 - 1772
361(chain C and (resseq -13:-7 or resseq 1:29 or resseq...C212 - 217
371(chain C and (resseq -13:-7 or resseq 1:29 or resseq...C-13 - 442
381(chain C and (resseq -13:-7 or resseq 1:29 or resseq...C212 - 217
391(chain C and (resseq -13:-7 or resseq 1:29 or resseq...C219 - 285
3101(chain C and (resseq -13:-7 or resseq 1:29 or resseq...C288 - 430
3111(chain C and (resseq -13:-7 or resseq 1:29 or resseq...C432 - 442
3121(chain C and (resseq -13:-7 or resseq 1:29 or resseq...C500 - 501

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Components

#1: Protein Methyltransferase domain-containing protein


Mass: 52095.387 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora carbonacea (bacteria) / Gene: GA0070563_112238 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1C5AE13
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
Sequence detailsResidues 100, 219, 232, and 444 are confirmed to be His, Thr, Ala, and Ser respectively. This was ...Residues 100, 219, 232, and 444 are confirmed to be His, Thr, Ala, and Ser respectively. This was verified by construct sequencing prior to the crystallization experiment.

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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: 3.96 Å3/Da / Density % sol: 68.94 % / Mosaicity: 0.501 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 22% PEG3350, 200 mM Li2SO4, 100 mM Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.918 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. obs: 34942 / % possible obs: 96.1 % / Redundancy: 7.1 % / Biso Wilson estimate: 121.83 Å2 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.024 / Rrim(I) all: 0.068 / Χ2: 1.263 / Net I/σ(I): 13.2 / Num. measured all: 248070
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.35-3.417.10.92617590.6690.3610.9981.21598.8
3.41-3.477.10.77117590.7460.3010.8311.22498.4
3.47-3.547.10.62217610.8450.2420.6711.23898.4
3.54-3.617.10.49117630.9190.190.5281.22698.2
3.61-3.697.10.3617620.9480.1390.3871.23598.3
3.69-3.777.20.27317460.9680.1050.2941.24797.8
3.77-3.877.10.25917510.9680.10.2791.28597.9
3.87-3.977.20.18717530.9860.0720.2011.2797.4
3.97-4.097.20.15617680.990.060.1681.28897.5
4.09-4.227.20.12817290.9920.0490.1371.32697.2
4.22-4.377.10.09617690.9950.0370.1041.28896.8
4.37-4.557.10.07817410.9960.030.0841.30396.7
4.55-4.757.20.06517380.9970.0250.071.29296.7
4.75-57.20.06117440.9970.0230.0661.3295.9
5-5.327.10.05717420.9980.0220.0621.31295.2
5.32-5.7370.05617310.9980.0220.0611.36895.4
5.73-6.370.0517260.9980.020.0541.35494.2
6.3-7.217.10.04217470.9990.0160.0461.28994
7.21-9.087.20.03317230.9990.0120.0351.1791.9
9.08-506.80.02717300.9990.0110.031.00487.6

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T38, 3BUS

5t38

3bus


Resolution: 3.35→45.641 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.12
RfactorNum. reflection% reflection
Rfree0.2664 1812 5.2 %
Rwork0.2207 --
obs0.2229 34838 95.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 284.89 Å2 / Biso mean: 140.0268 Å2 / Biso min: 79.75 Å2
Refinement stepCycle: final / Resolution: 3.35→45.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9698 0 45 0 9743
Biso mean--169.13 --
Num. residues----1243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029952
X-RAY DIFFRACTIONf_angle_d0.57513515
X-RAY DIFFRACTIONf_chiral_restr0.0431476
X-RAY DIFFRACTIONf_plane_restr0.0041794
X-RAY DIFFRACTIONf_dihedral_angle_d13.9635900
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5750X-RAY DIFFRACTION5.964TORSIONAL
12B5750X-RAY DIFFRACTION5.964TORSIONAL
13C5750X-RAY DIFFRACTION5.964TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.35-3.44060.34991280.34092555268399
3.4406-3.54180.41171290.31212607273699
3.5418-3.6560.33731410.27732540268198
3.656-3.78670.3151750.25552528270398
3.7867-3.93820.23651670.2432537270498
3.9382-4.11730.3171460.21152541268797
4.1173-4.33420.30411050.20272591269697
4.3342-4.60550.25081220.19462572269497
4.6055-4.96070.22741720.19292505267796
4.9607-5.45920.2321310.20632538266995
5.4592-6.24750.28761360.24022534267095
6.2475-7.86460.25561490.22932517266694
7.8646-45.64480.23821110.19772461257286
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)
12.9460.23770.41853.5448-0.94362.8748-0.02540.2552-0.19140.920.0148-0.55470.63450.03870.05441.5884-0.2667-0.22660.8065-0.10110.9151-29.720430.720218.0667
23.30680.35361.61593.044-0.11093.97320.1212-0.3991-0.41231.2418-0.13780.7613-0.3412-0.1221-0.06461.5125-0.43710.42051.1178-0.28511.3442-64.626811.902110.9851
34.1329-1.38680.94671.68490.20353.03290.28550.31770.0043-0.5170.21940.25150.2506-0.032-0.57631.1348-0.0898-0.32540.68490.24021.6958-12.26-13.189242.6915
43.38620.2391-0.08234.58620.76133.00510.2194-0.5407-0.890.25810.17790.0918-0.1763-1.1506-0.38220.95410.20370.16641.1570.49671.7334-33.998318.696854.0071
51.96390.33970.09973.210.56623.551-0.5-0.20890.5869-0.2201-0.04320.0965-0.42770.03640.51691.23930.3047-0.41031.0367-0.09130.9354-42.8631-17.3336-0.5525
62.7604-1.31741.29744.7427-0.40142.04720.2009-0.41520.02240.1462-0.64260.8651-0.2653-0.62860.42630.98820.2064-0.09161.8963-0.15570.8645-45.8757-30.730137.3809
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -13 through 231 )A-13 - 231
2X-RAY DIFFRACTION2chain 'A' and (resid 232 through 442 )A232 - 442
3X-RAY DIFFRACTION3chain 'B' and (resid -13 through 231 )B-13 - 231
4X-RAY DIFFRACTION4chain 'B' and (resid 232 through 442 )B232 - 442
5X-RAY DIFFRACTION5chain 'C' and (resid -13 through 231 )C-13 - 231
6X-RAY DIFFRACTION6chain 'C' and (resid 232 through 442 )C232 - 442

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