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- PDB-3kqq: Crystal Structure of hPNMT in Complex AdoHcy and 2-Hydroxynicotin... -

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Basic information

Entry
Database: PDB / ID: 3kqq
TitleCrystal Structure of hPNMT in Complex AdoHcy and 2-Hydroxynicotinic acid
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-oxo-1,2-dihydropyridine-3-carboxylic acid / S-ADENOSYL-L-HOMOCYSTEINE / Phenylethanolamine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / 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 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 6, 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)64,7396
Polymers63,6922
Non-polymers1,0474
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-13 kcal/mol
Surface area20010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.992, 93.992, 188.858
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-ES6 / 2-oxo-1,2-dihydropyridine-3-carboxylic acid


Mass: 139.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 62.44 %
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: 2.5→38.4 Å / Num. obs: 26826 / % possible obs: 89.2 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.117 / Χ2: 0.96 / Net I/σ(I): 7.3 / Scaling rejects: 1116
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.5-2.594.830.4292.61176724261.1182.4
2.59-2.695.880.40831643727771.1193.9
2.69-2.826.940.3593.52048029361.0699.8
2.82-2.966.950.2854.22069329651.0199.9
2.96-3.156.940.235.22058029490.9799.4
3.15-3.396.660.16171985129610.999.2
3.39-3.734.850.1138.61347227610.8192.3
3.73-4.273.90.07810.9990224900.8182.1
4.27-5.382.950.05813.4586719330.7663.2
5.38-38.43.580.02632949726280.7381

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Processing

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

1hnn


Resolution: 2.5→38.402 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.738 / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.306 1348 5.03 %Random
Rwork0.225 ---
obs0.229 26813 89.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.53 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso max: 120.43 Å2 / Biso mean: 51.975 Å2 / Biso min: 20.91 Å2
Baniso -1Baniso -2Baniso -3
1-4.166 Å20 Å2-0 Å2
2--4.166 Å2-0 Å2
3----8.332 Å2
Refinement stepCycle: LAST / Resolution: 2.5→38.402 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4099 0 72 135 4306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074282
X-RAY DIFFRACTIONf_angle_d1.0355829
X-RAY DIFFRACTIONf_chiral_restr0.069620
X-RAY DIFFRACTIONf_plane_restr0.005759
X-RAY DIFFRACTIONf_dihedral_angle_d20.9771589
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 (%)
2.5-2.5890.3681060.2542320242682
2.589-2.6930.3651500.2552627277794
2.693-2.8160.3321540.25627812935100
2.816-2.9640.3661160.25928472963100
2.964-3.150.341570.2612792294999
3.15-3.3930.3311600.242797295799
3.393-3.7340.2691510.2032609276092
3.734-4.2740.3051460.1932341248782
4.274-5.3820.258900.1831842193263
5.382-38.4060.221180.1772509262781
Refinement TLS params.Method: refined / Origin x: 24.2181 Å / Origin y: 51.3602 Å / Origin z: -5.5337 Å
111213212223313233
T0.2487 Å2-0.0336 Å2-0.0241 Å2-0.1675 Å20.0463 Å2--0.2595 Å2
L0.4051 °2-0.1199 °20.0919 °2-0.4175 °2-0.196 °2--0.9057 °2
S-0.0463 Å °0.0144 Å °0.0775 Å °0.0859 Å °-0.0148 Å °-0.0044 Å °-0.1194 Å °-0.0168 Å °0.0504 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 DIFFRACTION1allA2004 - 2163

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