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- PDB-3kpj: Crystal Structure of hPNMT in Complex AdoHcy and Bound Phosphate -

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Basic information

Entry
Database: PDB / ID: 3kpj
TitleCrystal Structure of hPNMT in Complex AdoHcy and Bound Phosphate
ComponentsPhenylethanolamine N-methyltransferase
KeywordsTRANSFERASE / methyltransferase / fragment screening / Catecholamine biosynthesis / S-adenosyl-L-methionine
Function / homology
Function and homology information


phenylethanolamine N-methyltransferase / phenylethanolamine N-methyltransferase activity / epinephrine biosynthetic process / Catecholamine biosynthesis / catecholamine biosynthetic process / methylation / cytosol
Similarity search - Function
Methyltransferase, NNMT/PNMT/TEMT / Methyltransferase NNMT/PNMT/TEMT, conserved site / : / NNMT/PNMT/TEMT family / NNMT/PNMT/TEMT family of methyltransferases signature. / SAM-dependent methyltransferase NNMT/PNMT/TEMT-type profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Phenylethanolamine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsDrinkwater, N. / Martin, J.L.
CitationJournal: Biochem.J. / Year: 2010
Title: Fragment-based screening by X-ray crystallography, MS and isothermal titration calorimetry to identify PNMT (phenylethanolamine N-methyltransferase) inhibitors.
Authors: Drinkwater, N. / Vu, H. / Lovell, K.M. / Criscione, K.R. / Collins, B.M. / Prisinzano, T.E. / Poulsen, S.A. / McLeish, M.J. / Grunewald, G.L. / Martin, J.L.
History
DepositionNov 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 4, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.type
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phenylethanolamine N-methyltransferase
B: Phenylethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6516
Polymers63,6922
Non-polymers9594
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-27 kcal/mol
Surface area20060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.420, 94.420, 186.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Phenylethanolamine N-methyltransferase / PNMTase / Noradrenaline N-methyltransferase


Mass: 31845.967 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PENT, PNMT / Plasmid: pET17 PNMT-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P11086, phenylethanolamine N-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.27 Å3/Da / Density % sol: 62.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: PEG6K, LiCl, cacodylate, pH 5.8, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Aug 3, 2007
RadiationMonochromator: HiRes2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→33.38 Å / Num. obs: 29790 / % possible obs: 99.1 % / Redundancy: 3.77 % / Rmerge(I) obs: 0.05 / Χ2: 0.97 / Net I/σ(I): 11.7 / Scaling rejects: 850
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.76 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2.2 / Num. measured all: 11110 / Num. unique all: 2933 / Χ2: 1.16 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata processing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1HNN

1hnn


Resolution: 2.5→33.383 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.765 / SU ML: 0.42 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1435 4.95 %random
Rwork0.211 ---
obs0.213 28975 96.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.753 Å2 / ksol: 0.312 e/Å3
Displacement parametersBiso max: 135.66 Å2 / Biso mean: 76.645 Å2 / Biso min: 42.63 Å2
Baniso -1Baniso -2Baniso -3
1-7.248 Å20 Å2-0 Å2
2--7.248 Å2-0 Å2
3----14.496 Å2
Refinement stepCycle: LAST / Resolution: 2.5→33.383 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4099 0 62 94 4255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074270
X-RAY DIFFRACTIONf_angle_d1.1215815
X-RAY DIFFRACTIONf_chiral_restr0.067630
X-RAY DIFFRACTIONf_plane_restr0.005759
X-RAY DIFFRACTIONf_dihedral_angle_d16.2641557
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.5890.4061440.3582650279495
2.589-2.6930.3441470.3162677282496
2.693-2.8160.3281260.2832715284196
2.816-2.9640.3331450.2542687283296
2.964-3.1490.3141350.2562712284796
3.149-3.3920.3271540.252737289197
3.392-3.7330.2771250.2122805293098
3.733-4.2730.2191660.1782772293897
4.273-5.3790.2251460.1562833297998
5.379-33.3860.2411470.1892952309996
Refinement TLS params.Method: refined / Origin x: 24.2957 Å / Origin y: 51.7534 Å / Origin z: -5.048 Å
111213212223313233
T0.4764 Å2-0.119 Å2-0.0834 Å2-0.4264 Å20.1536 Å2--0.52 Å2
L0.3983 °2-0.1155 °2-0.0215 °2-0.6778 °2-0.1815 °2--2.1949 °2
S-0.0687 Å °0.0038 Å °0.0516 Å °0.156 Å °-0.2014 Å °-0.1463 Å °-0.2722 Å °0.1148 Å °0.1852 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA24 - 280
2X-RAY DIFFRACTION1allB14 - 281
3X-RAY DIFFRACTION1allA - B3001 - 3002
4X-RAY DIFFRACTION1allA - B1 - 290
5X-RAY DIFFRACTION1allA1 - 337

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