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- PDB-3hcc: Crystal Structure of hPNMT in Complex With anti-9-amino-5-(triflu... -

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Basic information

Entry
Database: PDB / ID: 3hcc
TitleCrystal Structure of hPNMT in Complex With anti-9-amino-5-(trifluromethyl) benzonorbornene and AdoHcy
ComponentsPhenylethanolamine N-methyltransferase
KeywordsTRANSFERASE / methyltransferase / Catecholamine biosynthesis / Polymorphism / 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
Chem-LT3 / S-ADENOSYL-L-HOMOCYSTEINE / Phenylethanolamine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsDrinkwater, N. / Martin, J.L. / Gee, C.L. / Puri, M.
CitationJournal: Biochem.J. / Year: 2009
Title: Molecular recognition of physiological substrate noradrenaline by the adrenaline-synthesizing enzyme PNMT and factors influencing its methyltransferase activity.
Authors: Drinkwater, N. / Gee, C.L. / Puri, M. / Criscione, K.R. / McLeish, M.J. / Grunewald, G.L. / Martin, J.L.
History
DepositionMay 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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)64,9156
Polymers63,6922
Non-polymers1,2234
Water4,846269
1
A: Phenylethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4583
Polymers31,8461
Non-polymers6122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phenylethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4583
Polymers31,8461
Non-polymers6122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-13 kcal/mol
Surface area20030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.720, 94.720, 186.210
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-LT3 / (1S,4R,9S)-5-(trifluoromethyl)-1,2,3,4-tetrahydro-1,4-methanonaphthalen-9-amine


Mass: 227.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H12F3N
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 3.28 Å3/Da / Density % sol: 62.49 %
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 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 29, 2005
RadiationMonochromator: HiRes2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→29.95 Å / Num. obs: 38435 / Redundancy: 7.78 % / Biso Wilson estimate: 46.65 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.84 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 4.1

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1HNN

1hnn


Resolution: 2.3→29.95 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.817 / SU ML: 0.32 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.24 3831 10.02 %RANDOM
Rwork0.205 ---
obs0.208 38227 99.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.638 Å2 / ksol: 0.294 e/Å3
Displacement parametersBiso max: 126.73 Å2 / Biso mean: 58.034 Å2 / Biso min: 28.86 Å2
Baniso -1Baniso -2Baniso -3
1-7.622 Å20 Å2-0 Å2
2--7.622 Å2-0 Å2
3----15.243 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4126 0 84 269 4479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034326
X-RAY DIFFRACTIONf_angle_d0.9115901
X-RAY DIFFRACTIONf_chiral_restr0.056633
X-RAY DIFFRACTIONf_plane_restr0.007767
X-RAY DIFFRACTIONf_dihedral_angle_d18.971611
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.3290.3371450.33212521397100
2.329-2.360.3421340.32412501384100
2.36-2.3920.351470.32412481395100
2.392-2.4260.3411330.29612601393100
2.426-2.4630.3031380.28712561394100
2.463-2.5010.2731190.2812821401100
2.501-2.5420.3271520.2581236138899
2.542-2.5860.2721530.24412431396100
2.586-2.6330.3441400.2521266140699
2.633-2.6830.2921640.24612261390100
2.683-2.7380.2821460.241251139799
2.738-2.7980.3421330.23812821415100
2.798-2.8630.2941370.2141252138999
2.863-2.9340.2731180.2161275139399
2.934-3.0130.2691460.2011241138799
3.013-3.1020.2441460.2051274142099
3.102-3.2020.2651420.2081266140899
3.202-3.3160.2531410.2061257139899
3.316-3.4490.2441720.21234140699
3.449-3.6060.211460.17512871433100
3.606-3.7950.2161300.1781303143399
3.795-4.0330.2141300.1671268139899
4.033-4.3430.1991470.1661300144799
4.343-4.7790.1681490.1441297144699
4.779-5.4660.1811290.1611316144599
5.466-6.8730.2191340.1913611495100
6.873-29.9560.2081600.2081413157398
Refinement TLS params.Method: refined / Origin x: 24.4305 Å / Origin y: 51.7563 Å / Origin z: -5.1375 Å
111213212223313233
T0.2908 Å2-0.0504 Å2-0.0297 Å2-0.1998 Å20.0796 Å2--0.2533 Å2
L0.2845 °2-0.0188 °20.0148 °2-0.3466 °2-0.2794 °2--0.7179 °2
S-0.0479 Å °-0.0214 Å °0.032 Å °0.0957 Å °-0.0695 Å °-0.0181 Å °-0.1696 Å °0.0323 Å °0.0764 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA23 - 281
2X-RAY DIFFRACTION1allB14 - 281
3X-RAY DIFFRACTION1allA - B2001 - 2002
4X-RAY DIFFRACTION1allA - B3001 - 3002
5X-RAY DIFFRACTION1allB - A1 - 312

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