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- PDB-3kpy: Crystal Structure of hPNMT in Complex AdoHcy and 6-Chlorooxindole -

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Basic information

Entry
Database: PDB / ID: 3kpy
TitleCrystal Structure of hPNMT in Complex AdoHcy and 6-Chlorooxindole
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-chloro-1,3-dihydro-2H-indol-2-one / S-ADENOSYL-L-HOMOCYSTEINE / Phenylethanolamine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / 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

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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)64,7966
Polymers63,6922
Non-polymers1,1044
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-14 kcal/mol
Surface area19950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.908, 93.908, 188.615
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 / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-ES2 / 6-chloro-1,3-dihydro-2H-indol-2-one


Mass: 167.592 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H6ClNO
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O

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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: 3.26 Å3/Da / Density % sol: 62.32 %
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: Nov 6, 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→45.56 Å / Num. obs: 30511 / % possible obs: 90.2 % / Redundancy: 4.91 % / Rmerge(I) obs: 0.096 / Χ2: 0.96 / Net I/σ(I): 8.6 / Scaling rejects: 1134
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.4-2.493.850.2763.8954724781.175
2.49-2.594.480.2464.41300229001.0787.2
2.59-2.75.710.2414.91850032361.0697.7
2.7-2.856.850.26.1227033310199.1
2.85-3.026.740.1577.42216932860.9698.4
3.02-3.266.460.1239.12119932700.9397.6
3.26-3.585.060.08910.91636232040.8695.3
3.58-4.13.510.07311.71066729840.8787.7
4.1-5.172.80.06512.6789827300.979.3
5.17-45.562.80.03124.9902331130.885.5

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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
Resolution: 2.4→45.563 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.785 / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1583 5.19 %Random
Rwork0.206 ---
obs0.209 30500 90.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.791 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso max: 124.55 Å2 / Biso mean: 42.447 Å2 / Biso min: 18.22 Å2
Baniso -1Baniso -2Baniso -3
1-3.457 Å20 Å2-0 Å2
2--3.457 Å2-0 Å2
3----6.913 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4099 0 74 268 4441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054286
X-RAY DIFFRACTIONf_angle_d0.8675837
X-RAY DIFFRACTIONf_chiral_restr0.061620
X-RAY DIFFRACTIONf_plane_restr0.004759
X-RAY DIFFRACTIONf_dihedral_angle_d21.1011589
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.4770.2841340.2192109224374
2.477-2.5660.2851210.2132456257786
2.566-2.6690.3331690.2152732290196
2.669-2.790.3151550.2272824297999
2.79-2.9370.31280.2212889301799
2.937-3.1210.3521410.2282823296498
3.121-3.3620.3031730.2292816298998
3.362-3.70.2821430.1972685282892
3.7-4.2360.2471620.1822522268487
4.236-5.3350.2011230.172333245678
5.335-45.5710.2021340.1642728286286
Refinement TLS params.Method: refined / Origin x: 24.0715 Å / Origin y: 51.1323 Å / Origin z: -5.8487 Å
111213212223313233
T0.2152 Å2-0.0329 Å2-0.0206 Å2-0.1054 Å20.0373 Å2--0.2164 Å2
L0.3414 °2-0.0918 °2-0.016 °2-0.227 °2-0.2191 °2--0.9877 °2
S-0.0393 Å °-0.0041 Å °0.0878 Å °0.0723 Å °-0.0156 Å °-0.009 Å °-0.1676 Å °0.0309 Å °0.0431 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 DIFFRACTION1allA2003 - 2312

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