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- PDB-3kr2: Crystal Structure of hPNMT in Complex AdoHcy and 5-fluoro-1H-benz... -

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Basic information

Entry
Database: PDB / ID: 3kr2
TitleCrystal Structure of hPNMT in Complex AdoHcy and 5-fluoro-1H-benzo[d]imidazol-2-amine
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
6-fluoro-1H-benzimidazol-2-amine / S-ADENOSYL-L-HOMOCYSTEINE / Phenylethanolamine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.3 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 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / 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 1.3Oct 9, 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)64,7636
Polymers63,6922
Non-polymers1,0714
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-13 kcal/mol
Surface area20140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.426, 94.426, 188.185
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-ET2 / 6-fluoro-1H-benzimidazol-2-amine


Mass: 151.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6FN3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 3.29 Å3/Da / Density % sol: 62.65 %
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 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 4, 2000
RadiationMonochromator: HiRes2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→45.72 Å / Num. obs: 38507 / % possible obs: 99.7 % / Redundancy: 3.87 % / Rmerge(I) obs: 0.06 / Χ2: 0.98 / Net I/σ(I): 10 / Scaling rejects: 1127
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.3-2.383.890.4772.31475437721.14100
2.38-2.483.910.4212.51489237941.11100
2.48-2.593.910.3323.31483337801.1100
2.59-2.733.920.2434.11498338081.07100
2.73-2.93.910.1745.41500738230.98100
2.9-3.123.90.1177.41500538270.93100
3.12-3.443.920.08210.71517838530.8599.9
3.44-3.933.750.06314.31471538830.8499.5
3.93-4.953.890.0520.41529939070.8299.8
4.95-45.723.70.03229.51543940600.9497.9

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Processing

Software
NameVersionClassificationNB
d*TREK9.7 W8RSSIdata processing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementStarting model: PDB entry 1HNN

1hnn


Resolution: 2.3→45.717 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.789 / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1924 5.18 %Random
Rwork0.212 ---
obs0.214 37163 96.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso max: 140.1 Å2 / Biso mean: 60.298 Å2 / Biso min: 28.82 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4099 0 74 145 4318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084286
X-RAY DIFFRACTIONf_angle_d1.0895837
X-RAY DIFFRACTIONf_chiral_restr0.068620
X-RAY DIFFRACTIONf_plane_restr0.008761
X-RAY DIFFRACTIONf_dihedral_angle_d18.8891581
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.3580.3611330.332430256395
2.358-2.4210.3561350.3142436257195
2.421-2.4930.3111320.2742432256495
2.493-2.5730.2621330.2542488262196
2.573-2.6650.2881370.2452457259496
2.665-2.7720.3361320.2492478261095
2.772-2.8980.2851370.2432477261497
2.898-3.050.281350.2492496263196
3.05-3.2410.2791370.2412527266497
3.241-3.4920.3021400.2232525266597
3.492-3.8430.2441360.1992529266596
3.843-4.3990.2031430.172587273098
4.399-5.540.1751450.1572642278798
5.54-45.7260.211490.1882735288496
Refinement TLS params.Method: refined / Origin x: 24.3148 Å / Origin y: 51.3748 Å / Origin z: -5.4375 Å
111213212223313233
T0.4837 Å2-0.0464 Å2-0.0368 Å2-0.3711 Å20.0508 Å2--0.2401 Å2
L0.6046 °2-0.0823 °2-0.0142 °2-0.3837 °2-0.2241 °2--1.1193 °2
S-0.0593 Å °0.0141 Å °0.0548 Å °0.0578 Å °-0.0382 Å °0.0134 Å °-0.1467 Å °-0.0221 Å °0 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 - B1001 - 1002
5X-RAY DIFFRACTION1allB1 - 361

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