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- PDB-3kqy: Crystal Structure of hPNMT in Complex AdoHcy and 2-amino-1H-benzo... -

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Basic information

Entry
Database: PDB / ID: 3kqy
TitleCrystal Structure of hPNMT in Complex AdoHcy and 2-amino-1H-benzo[d]imidazol-7-ol
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
2-amino-1H-benzimidazol-7-ol / S-ADENOSYL-L-HOMOCYSTEINE / Phenylethanolamine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.2 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 16, 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)64,7596
Polymers63,6922
Non-polymers1,0674
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-14 kcal/mol
Surface area20140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.525, 94.525, 188.270
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-ES0 / 2-amino-1H-benzimidazol-7-ol


Mass: 149.150 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7N3O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 3.3 Å3/Da / Density % sol: 62.74 %
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: 2.2→47.26 Å / Num. obs: 44046 / % possible obs: 99.8 % / Redundancy: 4.19 % / Rmerge(I) obs: 0.056 / Χ2: 0.95 / Net I/σ(I): 10 / Scaling rejects: 1394
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.2-2.284.150.5032.11810843061.21100
2.28-2.374.190.422.51830443471.13100
2.37-2.484.20.3642.91839943531.11100
2.48-2.614.210.2643.91832643301.08100
2.61-2.774.220.1865.21855143780.99100
2.77-2.994.230.12971851843620.9100
2.99-3.294.220.088101868444040.84100
3.29-3.764.220.05715.11880744320.7699.9
3.76-4.744.20.04320.71901144870.7499.8
4.74-47.264.020.0329.71905346470.898.4

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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: 2.2→47.262 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.774 / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1928 4.56 %Random
Rwork0.228 ---
obs0.229 42314 95.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.022 Å2 / ksol: 0.312 e/Å3
Displacement parametersBiso max: 117.96 Å2 / Biso mean: 54.73 Å2 / Biso min: 24.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4099 0 74 162 4335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044293
X-RAY DIFFRACTIONf_angle_d0.9565848
X-RAY DIFFRACTIONf_chiral_restr0.063621
X-RAY DIFFRACTIONf_plane_restr0.008763
X-RAY DIFFRACTIONf_dihedral_angle_d18.7841586
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 (%)
2.2-2.2550.3721330.3412749288293
2.255-2.3160.3631300.3062747287793
2.316-2.3840.3181330.2842791292495
2.384-2.4610.2821370.2812790292795
2.461-2.5490.3171320.2642818295095
2.549-2.6510.321400.2752809294995
2.651-2.7720.3451370.2672857299496
2.772-2.9180.321360.272841297795
2.918-3.1010.351370.2632881301896
3.101-3.340.2951380.2562921305997
3.34-3.6760.2751380.2152974311298
3.676-4.2080.221450.1882994313998
4.208-5.30.2061410.1673040318199
5.3-47.2730.2011510.1963174332597
Refinement TLS params.Method: refined / Origin x: 24.3203 Å / Origin y: 51.4566 Å / Origin z: -5.6631 Å
111213212223313233
T0.2996 Å2-0.0239 Å2-0.0235 Å2-0.2205 Å20.0342 Å2--0.1229 Å2
L0.3016 °2-0.0505 °20.001 °2-0.1723 °2-0.1142 °2--0.1037 °2
S-0.0184 Å °0.0113 Å °0.0301 Å °0.0297 Å °-0.0218 Å °0.0081 Å °-0.0452 Å °-0.0114 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 - B1 - 290
5X-RAY DIFFRACTION1allA1 - 363

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