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- PDB-3kpu: Crystal Structure of hPNMT in Complex AdoHcy and 4-quinolinol -

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Basic information

Entry
Database: PDB / ID: 3kpu
TitleCrystal Structure of hPNMT in Complex AdoHcy and 4-quinolinol
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
quinolin-4-ol / S-ADENOSYL-L-HOMOCYSTEINE / Phenylethanolamine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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 1.4Nov 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)64,7516
Polymers63,6922
Non-polymers1,0594
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-13 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.345, 94.345, 188.513
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: PNMT, PENT / 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-ES1 / quinolin-4-ol


Mass: 145.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H7NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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 FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 7, 2007
RadiationMonochromator: OSMIC VARI-MAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→35.03 Å / Num. obs: 31980 / % possible obs: 93.8 % / Redundancy: 4.69 % / Rmerge(I) obs: 0.151 / Χ2: 0.98 / Net I/σ(I): 5.3 / Scaling rejects: 1134
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.4-2.493.170.4362.2942929681.188.3
2.49-2.593.960.4012.71257531641.0996.1
2.59-2.75.440.3733.21850033741.1599.6
2.7-2.856.70.3263.6223923339199.9
2.85-3.026.530.2564.32203833680.9599.9
3.02-3.266.330.1975.32150933920.89100
3.26-3.585.210.1476.41753333460.8799
3.58-4.13.530.1117.81133331590.9691.6
4.1-5.172.660.0898.7757727670.8880.1
5.17-35.032.550.04715.9824831030.8784.6

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Processing

Software
NameVersionClassificationNB
d*TREK9.7 W8RSSIdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
JDirectordata collection
d*TREKdata reduction
MIFitphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HNN

1hnn


Resolution: 2.4→35.029 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.759 / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.291 1644 5.14 %Random
Rwork0.227 ---
obs0.23 31977 93.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.034 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso max: 129.63 Å2 / Biso mean: 49.738 Å2 / Biso min: 21.9 Å2
Baniso -1Baniso -2Baniso -3
1-4.152 Å20 Å2-0 Å2
2--4.152 Å2-0 Å2
3----8.305 Å2
Refinement stepCycle: LAST / Resolution: 2.4→35.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4099 0 74 205 4378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074286
X-RAY DIFFRACTIONf_angle_d15835
X-RAY DIFFRACTIONf_chiral_restr0.068620
X-RAY DIFFRACTIONf_plane_restr0.005759
X-RAY DIFFRACTIONf_dihedral_angle_d21.251581
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.4710.3581230.282309243287
2.471-2.550.3131320.2552496262894
2.55-2.6410.3621410.252615275699
2.641-2.7470.3181620.23526302792100
2.747-2.8720.3521320.24126522784100
2.872-3.0230.3361210.24627002821100
3.023-3.2130.3321530.25426642817100
3.213-3.4610.31460.23726672813100
3.461-3.8090.2581540.1962539269395
3.809-4.3590.3011430.1932394253788
4.359-5.4880.2081110.1852170228178
5.488-35.0330.2041260.1752497262385
Refinement TLS params.Method: refined / Origin x: 24.3788 Å / Origin y: 51.4416 Å / Origin z: -5.7917 Å
111213212223313233
T0.2871 Å2-0.033 Å2-0.0043 Å2-0.2137 Å20.045 Å2--0.3055 Å2
L0.3848 °2-0.1157 °20.0041 °2-0.3841 °2-0.2531 °2--0.8942 °2
S-0.0255 Å °0.0086 Å °0.052 Å °0.0744 Å °-0.0071 Å °0.0226 Å °-0.138 Å °0.0224 Å °0.0247 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA24 - 280
2X-RAY DIFFRACTION1allB14 - 281
3X-RAY DIFFRACTION1allA - B2001 - 2002
4X-RAY DIFFRACTION1allA - B1 - 290
5X-RAY DIFFRACTION1allB - A2004 - 2245

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