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- PDB-4dm3: Crystal structure of human PNMT in complex adohcy, resorcinol and... -

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Basic information

Entry
Database: PDB / ID: 4dm3
TitleCrystal structure of human PNMT in complex adohcy, resorcinol and imidazole
ComponentsPhenylethanolamine N-methyltransferase
KeywordsTRANSFERASE
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
IMIDAZOLE / RESORCINOL / S-ADENOSYL-L-HOMOCYSTEINE / Phenylethanolamine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / PDB ENTRY 3KPY / Resolution: 2.4001 Å
AuthorsNair, P.C. / Malde, A.K. / Mark, A.E.
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
DepositionFeb 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Jan 24, 2018Group: Advisory / Structure summary / Category: audit_author / pdbx_unobs_or_zero_occ_atoms / Item: _audit_author.name
Remark 0THIS ENTRY 4DM3 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R3KPYSF) ...THIS ENTRY 4DM3 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R3KPYSF) DETERMINED BY AUTHORS OF THE PDB ENTRY 3KPY:
Remark 200AUTHOR USED THE SF DATA FROM ENTRY 3KPY.

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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)64,8198
Polymers63,6922
Non-polymers1,1276
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint7 kcal/mol
Surface area19870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.908, 93.908, 188.615
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: 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


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-RCO / RESORCINOL / 1,3-BENZENEDIOL / 1,3-DIHYDROXYBENZENE


Mass: 110.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6O2
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.45 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→45.563 Å / Num. obs: 30511 / % possible obs: 90.2 % / Redundancy: 4.91 % / Rmerge(I) obs: 0.096
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.276 / % possible all: 75

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.6_289) / Classification: refinement
RefinementMethod to determine structure: PDB ENTRY 3KPY / Resolution: 2.4001→45.563 Å / SU ML: 0.37 / σ(F): 1.33 / Phase error: 27.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2752 1583 5.19 %
Rwork0.2199 --
obs0.2227 30487 90.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.245 Å2 / ksol: 0.319 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.5704 Å20 Å2-0 Å2
2--3.5704 Å20 Å2
3----7.1409 Å2
Refinement stepCycle: LAST / Resolution: 2.4001→45.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4099 0 78 201 4378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094303
X-RAY DIFFRACTIONf_angle_d1.155851
X-RAY DIFFRACTIONf_dihedral_angle_d16.9271556
X-RAY DIFFRACTIONf_chiral_restr0.076630
X-RAY DIFFRACTIONf_plane_restr0.005764
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.48580.28661420.23562336X-RAY DIFFRACTION75
2.4858-2.58540.29741510.24052748X-RAY DIFFRACTION87
2.5854-2.7030.34071740.24183061X-RAY DIFFRACTION98
2.703-2.84550.30661660.24333142X-RAY DIFFRACTION99
2.8455-3.02370.33171460.24853137X-RAY DIFFRACTION98
3.0237-3.25710.33081750.25373091X-RAY DIFFRACTION97
3.2571-3.58480.2911710.22213031X-RAY DIFFRACTION95
3.5848-4.10320.261750.19892807X-RAY DIFFRACTION88
4.1032-5.16850.20321300.192600X-RAY DIFFRACTION79
5.1685-45.57160.20841530.1732951X-RAY DIFFRACTION85

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