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- PDB-6wlf: Phosphoethanolamine Methyltransferase from the Pine Wilt Nematode... -

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Basic information

Entry
Database: PDB / ID: 6wlf
TitlePhosphoethanolamine Methyltransferase from the Pine Wilt Nematode Bursaphelenchus xylophilus
ComponentsPhosphoethanolamine N-methyltransferase 1
KeywordsTRANSFERASE / S-adenosylmethionine
Function / homologyMethyltransferase domain 25 / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER / S-ADENOSYL-L-HOMOCYSTEINE / (pine wood nematode) hypothetical protein
Function and homology information
Biological speciesBursaphelenchus xylophilus (pine wood nematode)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsLee, S.G. / Jez, J.M.
Funding support2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)NIH-AI-097119
Department of Energy (DOE, United States)DE-AC02-06CH11357
CitationJournal: Mol.Biochem.Parasitol. / Year: 2020
Title: Structural and biochemical analysis of phosphoethanolamine methyltransferase from the pine wilt nematode Bursaphelenchus xylophilus.
Authors: Lee, S.G. / Chung, M.S. / DeMarsilis, A.J. / Holland, C.K. / Jaswaney, R.V. / Jiang, C. / Kroboth, J.H.P. / Kulshrestha, K. / Marcelo, R.Z.W. / Meyyappa, V.M. / Nelson, G.B. / Patel, J.K. / ...Authors: Lee, S.G. / Chung, M.S. / DeMarsilis, A.J. / Holland, C.K. / Jaswaney, R.V. / Jiang, C. / Kroboth, J.H.P. / Kulshrestha, K. / Marcelo, R.Z.W. / Meyyappa, V.M. / Nelson, G.B. / Patel, J.K. / Petronio, A.J. / Powers, S.K. / Qin, P.R. / Ramachandran, M. / Rayapati, D. / Rincon, J.A. / Rocha, A. / Ferreira, J.G.R.N. / Steinbrecher, M.K. / Yao, K. / Zhang, E.J. / Zou, A.J. / Gang, M. / Sparks, M. / Cascella, B. / Cruz, W. / Jez, J.M.
History
DepositionApr 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 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: Phosphoethanolamine N-methyltransferase 1
B: Phosphoethanolamine N-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,2136
Polymers102,1622
Non-polymers1,0514
Water6,630368
1
A: Phosphoethanolamine N-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6063
Polymers51,0811
Non-polymers5252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphoethanolamine N-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6063
Polymers51,0811
Non-polymers5252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.948, 98.259, 164.954
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 Phosphoethanolamine N-methyltransferase 1


Mass: 51080.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bursaphelenchus xylophilus (pine wood nematode)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A1I7RPU0
#2: Chemical ChemComp-OPE / PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER / COLAMINE PHOSPHORIC ACID


Mass: 141.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H8NO4P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.53 Å3/Da / Density % sol: 51.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.2 M potassium phosphate (dibasic)/0.8 M sodium phosphate (monobasic) and 0.1 M sodium acetate/acetic acid, pH 4.5) with 5 mM pEA and 0.5 mM SAH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.05→48 Å / Num. obs: 66561 / % possible obs: 99.2 % / Redundancy: 7 % / Rsym value: 0.092 / Net I/σ(I): 23.8
Reflection shellResolution: 2.05→2.09 Å / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4273 / % possible all: 94.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KRG

4krg


Resolution: 2.05→47.983 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2034 2000 3.01 %
Rwork0.17 --
obs0.171 66471 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→47.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7031 0 0 368 7399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077218
X-RAY DIFFRACTIONf_angle_d0.8249812
X-RAY DIFFRACTIONf_dihedral_angle_d3.534262
X-RAY DIFFRACTIONf_chiral_restr0.0521085
X-RAY DIFFRACTIONf_plane_restr0.0041242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.1010.28261330.25344273X-RAY DIFFRACTION93
2.101-2.15780.29151360.2334388X-RAY DIFFRACTION96
2.1578-2.22130.25731410.21834535X-RAY DIFFRACTION99
2.2213-2.2930.20881410.20024570X-RAY DIFFRACTION100
2.293-2.37490.25441420.1884581X-RAY DIFFRACTION100
2.3749-2.470.22261440.18254621X-RAY DIFFRACTION100
2.47-2.58240.24231430.18494610X-RAY DIFFRACTION100
2.5824-2.71860.24171430.17934608X-RAY DIFFRACTION100
2.7186-2.88890.21411430.17784632X-RAY DIFFRACTION100
2.8889-3.11190.22631450.17584660X-RAY DIFFRACTION100
3.1119-3.4250.18481440.16684648X-RAY DIFFRACTION100
3.425-3.92040.19411460.1564693X-RAY DIFFRACTION100
3.9204-4.93850.17641460.13284739X-RAY DIFFRACTION100
4.9385-47.9830.1711530.16844913X-RAY DIFFRACTION100
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)
11.6828-0.5770.19682.80730.6522.48920.0761-0.2110.20520.3501-0.10110.105-0.2812-0.07390.02880.3935-0.03060.05680.2098-0.0130.2499-3.4140.549-22.1935
23.7487-0.44820.63273.06070.0022.9738-0.0098-0.41840.04080.5739-0.08270.2907-0.1214-0.18120.06470.4243-0.06310.08880.2346-0.02380.2313-6.485729.6916-17.1599
33.002-0.82820.23712.96480.11292.29130.1558-0.2177-0.33060.3676-0.11660.50950.12-0.3942-0.02290.3404-0.05520.05140.2369-0.0090.2785-9.332721.3608-21.7122
40.28820.3268-0.12761.8490.36323.39110.0605-0.2019-0.17080.4716-0.0380.00360.29150.1901-0.06890.3206-0.0839-0.06310.31850.07890.33820.66465.666-21.4673
53.84591.2029-0.84575.1570.52632.9406-0.08180.0518-0.184-0.05460.0219-0.28410.18840.08950.07380.2588-0.0057-0.02270.17730.01070.24173.739410.1414-32.3138
62.0141-0.2702-0.20846.63951.27792.7821-0.01040.0176-0.0587-0.2633-0.18490.1968-0.0105-0.22360.19460.3229-0.0298-0.02420.2969-0.01040.2522-5.59932.5494-43.0031
73.24761.29140.35022.84720.00552.5453-0.34920.4841-0.1214-0.79490.30330.11960.1782-0.1820.05550.5662-0.15920.01360.43460.01390.2829-34.1321-24.227-23.5715
82.10181.2562-0.17492.16380.18091.647-0.31220.35170.1651-0.63340.1876-0.04110.0143-0.09470.14520.4758-0.02910.06940.30460.04650.3144-19.0411-10.6957-20.4935
91.35690.59480.05591.59070.16442.6755-0.1432-0.023-0.229-0.0534-0.0163-0.44820.19880.32230.12760.30490.04320.05160.26610.0620.3494-10.912-13.7253-6.9992
103.28591.6038-0.22163.98550.22223.10630.0618-0.27520.14010.3681-0.2468-0.068-0.33630.12960.18070.37360.0438-0.00120.26870.04410.2322-12.6995-0.79661.6759
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 108 )
2X-RAY DIFFRACTION2chain 'A' and (resid 109 through 175 )
3X-RAY DIFFRACTION3chain 'A' and (resid 176 through 242 )
4X-RAY DIFFRACTION4chain 'A' and (resid 243 through 281 )
5X-RAY DIFFRACTION5chain 'A' and (resid 282 through 350 )
6X-RAY DIFFRACTION6chain 'A' and (resid 351 through 454 )
7X-RAY DIFFRACTION7chain 'B' and (resid 9 through 175 )
8X-RAY DIFFRACTION8chain 'B' and (resid 176 through 281 )
9X-RAY DIFFRACTION9chain 'B' and (resid 282 through 350 )
10X-RAY DIFFRACTION10chain 'B' and (resid 351 through 454 )

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