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- PDB-4mq4: Crystal Structure of hPNMT in Complex with bisubstrate inhibitor ... -

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Basic information

Entry
Database: PDB / ID: 4mq4
TitleCrystal Structure of hPNMT in Complex with bisubstrate inhibitor N-(3-((((2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl)thio)propyl)-1,2,3,4-tetrahydroisoquinoline-3-carboxamide
ComponentsPhenylethanolamine N-methyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / adrenaline synthesis / methyltransferase / transferase-transferase inhibitor complex
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-2D5 / Phenylethanolamine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2042 Å
AuthorsBart, A.G. / Scott, E.E.
CitationJournal: To be Published
Title: To be Published
Authors: Bart, A.G. / Scott, E.E.
History
DepositionSep 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Derived calculations / Category: struct_conn

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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)64,9356
Polymers63,6922
Non-polymers1,2434
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-3 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.15, 94.15, 188.16
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: pET17PNMT-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysE
References: UniProt: P11086, phenylethanolamine N-methyltransferase
#2: Chemical ChemComp-2D5 / 5'-S-(3-{[(3R)-1,2,3,4-tetrahydroisoquinolin-3-ylcarbonyl]amino}propyl)-5'-thioadenosine


Mass: 499.586 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H29N7O4S
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 3.27 Å3/Da / Density % sol: 62.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M Na cacodylate pH 5.6, 0.17 M LiCl, 9% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2013 / Details: RH COATED MIRROR, K-B FOCUSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.2→38.432 Å / Num. obs: 43470 / % possible obs: 99.8 %

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2042→38.432 Å / SU ML: 0.26 / Phase error: 26.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2207 2191 5.07 %RANDOM
Rwork0.1806 ---
obs0.1826 43250 99.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2042→38.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4063 0 86 181 4330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134368
X-RAY DIFFRACTIONf_angle_d1.4435953
X-RAY DIFFRACTIONf_chiral_restr0.081638
X-RAY DIFFRACTIONf_plane_restr0.008766
X-RAY DIFFRACTIONf_dihedral_angle_d18.1321627
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2042-2.25210.37071560.30922449260598
2.2521-2.30450.31941310.27242518264999
2.3045-2.36210.32631410.238125192660100
2.3621-2.42590.30791360.23472533266999
2.4259-2.49730.25971300.223825142644100
2.4973-2.57790.31211020.214525632665100
2.5779-2.670.25461080.21082565267399
2.67-2.77690.26971480.20942550269899
2.7769-2.90320.24711240.20322522264699
2.9032-3.05620.24511410.206125882729100
3.0562-3.24760.26061440.201125632707100
3.2476-3.49820.25191360.191325792715100
3.4982-3.850.22581290.172625832712100
3.85-4.40640.18021810.147525782759100
4.4064-5.54890.16621560.14392634279099
5.5489-38.43730.18811280.16372801292999

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