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- PDB-4kri: Haemonchus contortus Phospholethanolamine N-methyltransferase 2 i... -

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Basic information

Entry
Database: PDB / ID: 4kri
TitleHaemonchus contortus Phospholethanolamine N-methyltransferase 2 in complex with phosphomonomethylethanolamine and S-adenosylhomocysteine
ComponentsPhospholethanolamine N-methyltransferase 2
KeywordsTRANSFERASE / methyltransferase
Function / homology
Function and homology information


phosphoethanolamine N-methyltransferase / S-adenosylmethionine-dependent methyltransferase activity
Similarity search - Function
Phosphoethanolamine N-methyltransferase 2, N-terminal / Phosphoethanolamine N-methyltransferase 2 N-terminal / Methyltransferase type 11 / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
2-(methylamino)ethyl dihydrogen phosphate / S-ADENOSYL-L-HOMOCYSTEINE / phosphoethanolamine N-methyltransferase
Similarity search - Component
Biological speciesHaemonchus contortus (barber pole worm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsLee, S.G. / Jez, J.M.
CitationJournal: Structure / Year: 2013
Title: Evolution of structure and mechanistic divergence in di-domain methyltransferases from nematode phosphocholine biosynthesis.
Authors: Lee, S.G. / Jez, J.M.
History
DepositionMay 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospholethanolamine N-methyltransferase 2
B: Phospholethanolamine N-methyltransferase 2
C: Phospholethanolamine N-methyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,3509
Polymers148,7323
Non-polymers1,6196
Water18,1051005
1
A: Phospholethanolamine N-methyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1173
Polymers49,5771
Non-polymers5402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phospholethanolamine N-methyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1173
Polymers49,5771
Non-polymers5402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Phospholethanolamine N-methyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1173
Polymers49,5771
Non-polymers5402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.987, 136.838, 90.867
Angle α, β, γ (deg.)90.00, 118.39, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-918-

HOH

21C-832-

HOH

31C-858-

HOH

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Components

#1: Protein Phospholethanolamine N-methyltransferase 2


Mass: 49577.199 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemonchus contortus (barber pole worm)
Plasmid: pET-28a-HcPMT2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta II (DE3) / References: UniProt: U5HK48*PLUS
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-1SH / 2-(methylamino)ethyl dihydrogen phosphate


Mass: 155.090 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H10NO4P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1005 / 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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M sodium citrate, 20% PEG-3,000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 10, 2010
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.72→34.2 Å / Num. all: 150732 / Num. obs: 150007 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→34.2 Å / SU ML: 0.19 / σ(F): 1.35 / Phase error: 21.42 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2101 7528 5.02 %random
Rwork0.1745 ---
obs0.1762 150007 97.45 %-
all-150732 --
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.517 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.8558 Å20 Å2-0.5396 Å2
2--7.7785 Å20 Å2
3----0.9228 Å2
Refinement stepCycle: LAST / Resolution: 1.72→34.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10342 0 105 1005 11452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610711
X-RAY DIFFRACTIONf_angle_d1.03614441
X-RAY DIFFRACTIONf_dihedral_angle_d17.3534067
X-RAY DIFFRACTIONf_chiral_restr0.0791547
X-RAY DIFFRACTIONf_plane_restr0.0051856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.74170.2792360.25494146X-RAY DIFFRACTION86
1.7417-1.76210.29332330.25394720X-RAY DIFFRACTION97
1.7621-1.78360.28592530.23784702X-RAY DIFFRACTION96
1.7836-1.80620.26732220.22114728X-RAY DIFFRACTION97
1.8062-1.830.24042320.20824684X-RAY DIFFRACTION97
1.83-1.8550.25672610.20934747X-RAY DIFFRACTION97
1.855-1.88150.27832400.20864669X-RAY DIFFRACTION97
1.8815-1.90960.24792450.19714719X-RAY DIFFRACTION97
1.9096-1.93950.23462600.18734727X-RAY DIFFRACTION97
1.9395-1.97130.23412750.18884761X-RAY DIFFRACTION98
1.9713-2.00520.22752450.1864772X-RAY DIFFRACTION98
2.0052-2.04170.23862520.18494766X-RAY DIFFRACTION98
2.0417-2.0810.22542720.1864749X-RAY DIFFRACTION98
2.081-2.12340.22782400.18384767X-RAY DIFFRACTION98
2.1234-2.16960.20922520.18284795X-RAY DIFFRACTION99
2.1696-2.22010.22442550.17864815X-RAY DIFFRACTION99
2.2201-2.27560.20312410.16854797X-RAY DIFFRACTION99
2.2756-2.33710.19732400.16824833X-RAY DIFFRACTION99
2.3371-2.40580.23672650.17244818X-RAY DIFFRACTION99
2.4058-2.48350.23142970.17734763X-RAY DIFFRACTION99
2.4835-2.57220.21632530.17494839X-RAY DIFFRACTION99
2.5722-2.67520.22612460.17514817X-RAY DIFFRACTION99
2.6752-2.79690.21952810.18154780X-RAY DIFFRACTION99
2.7969-2.94420.22532620.18644825X-RAY DIFFRACTION99
2.9442-3.12860.21042520.18144845X-RAY DIFFRACTION99
3.1286-3.36990.21942430.18184861X-RAY DIFFRACTION99
3.3699-3.70870.18652350.16424873X-RAY DIFFRACTION99
3.7087-4.24450.18472640.1464846X-RAY DIFFRACTION99
4.2445-5.34440.16992510.14664844X-RAY DIFFRACTION98
5.3444-34.21620.19552250.18124471X-RAY DIFFRACTION90
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)
10.7890.0369-0.4450.6313-0.04391.3055-0.0191-0.04320.1266-0.00870.0653-0.1408-0.10970.16400.1658-0.0076-0.0190.1442-0.02020.215221.7787-34.014911.2147
21.7302-0.22020.44991.36360.30160.8801-0.0235-0.21180.144-0.0076-0.07610.2519-0.0676-0.0635-0.14890.16720.0541-0.02280.1485-0.07050.2568-6.2108-41.075223.2973
30.95960.0292-0.39341.1219-0.0991.0054-0.1058-0.266-0.16610.3608-0.05280.27590.2995-0.1078-0.00320.47730.04550.0760.29950.0160.27259.5271-72.746541.7817
40.8566-0.7039-0.00581.73260.60030.65710.0207-0.0162-0.07050.0517-0.0088-0.08460.07910.1041-0.00110.22490.0713-0.01320.19370.00680.203627.9429-73.218416.5065
51.6824-0.4389-0.49510.84230.09030.4773-0.04030.541-0.3392-0.0282-0.07070.20030.0508-0.091-0.00420.1728-0.04760.02430.3493-0.08070.24192.6148-45.127567.8873
61.51480.208-1.20061.1086-0.2841.8605-0.01960.4485-0.051-0.17360.06550.0318-0.0146-0.27240.0230.195-0.01760.01990.3605-0.01640.121730.5308-35.909256.9712
74.7520.6727-3.63781.11670.35373.5234-0.0163-0.12590.2890.04090.0707-0.2610.04010.075-0.0337-0.16690.45920.01450.0376-0.26820.3199-10.0689-33.345325.6712
81.80871.7986-0.34612.31520.49761.4127-0.1646-0.03270.05870.0058-0.0001-0.05190.0421-0.00770.00090.1880.2063-0.07540.1318-0.1070.344734.8721-78.616618.3314
92.5762-0.3082-3.21020.10150.60754.769-0.00770.01080.01320.01450.00340.01810.012-0.13270.01050.2352-0.0190.06230.5033-0.05410.125431.0315-38.737248.4127
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:166)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 171:431)
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 2:165)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 171:431)
5X-RAY DIFFRACTION5CHAIN C AND (RESSEQ 1:165)
6X-RAY DIFFRACTION6CHAIN C AND (RESSEQ 172:431)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 702:702)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 702:702)
9X-RAY DIFFRACTION9CHAIN C AND (RESSEQ 702:702)

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