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- PDB-1n7i: The structure of Phenylethanolamine N-methyltransferase in comple... -

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Basic information

Entry
Database: PDB / ID: 1n7i
TitleThe structure of Phenylethanolamine N-methyltransferase in complex with S-adenosylhomocysteine and the inhibitor LY134046
ComponentsPhenylethanolamine N-methyltransferase
KeywordsTRANSFERASE / methyltransferase / catecholamine / adrenaline / epinephrine / s-adenosylmethionine / s-adenolsylhomocysteine
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
Chem-LY1 / S-ADENOSYL-L-HOMOCYSTEINE / Phenylethanolamine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Difference fourier / Resolution: 2.8 Å
AuthorsMcMillan, F.M. / Archbold, J. / McLeish, M.J. / Caine, J.M. / Criscione, K.R. / Grunewald, G.L. / Martin, J.L.
CitationJournal: J.Med.Chem. / Year: 2004
Title: Molecular recognition of sub-micromolar inhibitors by the epinephrine-synthesizing enzyme phenylethanolamine N-methyltransferase.
Authors: McMillan, F.M. / Archbold, J. / McLeish, M.J. / Caine, J.M. / Criscione, K.R. / Grunewald, G.L. / Martin, J.L.
History
DepositionNov 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands / _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

Downloads & links

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Assembly

Deposited unit
A: Phenylethanolamine N-methyltransferase
B: Phenylethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9776
Polymers61,7762
Non-polymers1,2014
Water57632
1
A: Phenylethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4893
Polymers30,8881
Non-polymers6012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phenylethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4893
Polymers30,8881
Non-polymers6012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.350, 94.350, 186.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Phenylethanolamine N-methyltransferase / / PNMTase / Noradrenaline N-methyltransferase


Mass: 30887.982 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PNMT OR PENT / Plasmid: pET17 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
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-LY1 / 8,9-DICHLORO-2,3,4,5-TETRAHYDRO-1H-BENZO[C]AZEPINE


Mass: 216.107 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H11Cl2N
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 3.55 Å3/Da / Density % sol: 65.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: PEG 6K, lithium chloride, cacodylate, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / PH range low: 6.25 / PH range high: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
111 mMdithiothreitol1drop
22 mMAdoHcy1drop
315 mM8,9-dichloro-2,3,4,5-tetrahydro-1H-2-benzazepine1drop
40.1 Mcacodylate1reservoirpH6-6.25
56-10 %PEG60001reservoir
60.25 M1reservoirLiCl
780 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 31, 1997 / Details: Yale mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→34.92 Å / Num. all: 21507 / Num. obs: 20430 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 68.8 Å2 / Limit h max: 33 / Limit h min: 1 / Limit k max: 23 / Limit k min: 1 / Limit l max: 65 / Limit l min: 0 / Observed criterion F max: 1528925.42 / Observed criterion F min: 7.9 / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.4
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 2.5 / % possible all: 89
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 50 Å / Num. measured all: 80055
Reflection shell
*PLUS
% possible obs: 89 %

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: Difference fourier / Resolution: 2.8→34.92 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.281 2008 9.8 %random
Rwork0.227 ---
all0.238 21507 --
obs0.238 20416 94.9 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 23.3335 Å2 / ksol: 0.310044 e/Å3
Displacement parametersBiso max: 83.78 Å2 / Biso mean: 49.83 Å2 / Biso min: 19.46 Å2
Baniso -1Baniso -2Baniso -3
1-3.88 Å20 Å20 Å2
2--3.88 Å20 Å2
3----7.75 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
nonpolymerX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.51 Å
Luzzati d res high-2.8
Refinement stepCycle: LAST / Resolution: 2.8→34.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4063 0 78 32 4173
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg23.7
X-RAY DIFFRACTIONx_torsion_impr_deg0.98
X-RAY DIFFRACTIONx_mcbond_it1.041.5
X-RAY DIFFRACTIONx_mcangle_it1.822
X-RAY DIFFRACTIONx_scbond_it1.492
X-RAY DIFFRACTIONx_scangle_it2.362.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.8-2.930.3532319.80.32521230.0232637235489.2
2.93-3.080.35424310.10.30621610.0232630240491.4
3.08-3.270.321271110.27621990.0192653247093.1
3.27-3.530.3042409.60.25122720.022633251295.4
3.53-3.880.27823490.2223560.0182666259097.1
3.88-4.440.272539.70.20323580.0172688261197.1
4.44-5.590.2422579.60.18924160.0152726267398.1
5.59-34.920.261279100.20725230.0162885280297.1
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ly_jlm.top
X-RAY DIFFRACTION4sah.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.54
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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