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- PDB-1hnn: CRYSTAL STRUCTURE OF HUMAN PNMT COMPLEXED WITH SK&F 29661 AND ADO... -

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Basic information

Entry
Database: PDB / ID: 1hnn
TitleCRYSTAL STRUCTURE OF HUMAN PNMT COMPLEXED WITH SK&F 29661 AND ADOHCY(SAH)
ComponentsPHENYLETHANOLAMINE N-METHYLTRANSFERASE
KeywordsTRANSFERASE / methyltransferase / adrenaline synthesis / S-adenosyl 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
S-ADENOSYL-L-HOMOCYSTEINE / Chem-SKF / Phenylethanolamine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.4 Å
AuthorsMartin, J.L. / Begun, J. / McLeish, M.J. / Caine, J.M. / Grunewald, G.L.
CitationJournal: Structure / Year: 2001
Title: Getting the adrenaline going: crystal structure of the adrenaline-synthesizing enzyme PNMT.
Authors: Martin, J.L. / Begun, J. / McLeish, M.J. / Caine, J.M. / Grunewald, G.L.
History
DepositionDec 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)62,9696
Polymers61,7762
Non-polymers1,1934
Water2,270126
1
A: PHENYLETHANOLAMINE N-METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4853
Polymers30,8881
Non-polymers5972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PHENYLETHANOLAMINE N-METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4853
Polymers30,8881
Non-polymers5972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.350, 94.350, 187.700
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


Mass: 30887.982 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PNMT / Production host: Escherichia coli (E. coli)
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-SKF / 1,2,3,4-TETRAHYDRO-ISOQUINOLINE-7-SULFONIC ACID AMIDE


Mass: 212.269 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12N2O2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 3.38 Å3/Da / Density % sol: 63.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 6K, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDCommon nameCrystal-IDSol-IDChemical formula
1PEG600011
211LiCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 14, 1997 / Details: Yale mirrors
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→38.48 Å / Num. all: 38545 / Num. obs: 34845 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 43.5 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 18.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 2.1 / % possible all: 54
Reflection
*PLUS
Lowest resolution: 50 Å
Reflection shell
*PLUS
% possible obs: 54 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS0.9refinement
RefinementMethod to determine structure: MIR / Resolution: 2.4→38.48 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 444544.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 3236 10 %RANDOM
Rwork0.23 ---
obs0.232 32279 95 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.19 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso mean: 45 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.4→38.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4154 0 80 126 4360
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it2.062
X-RAY DIFFRACTIONc_scbond_it1.772
X-RAY DIFFRACTIONc_scangle_it2.652.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.367 460 10.4 %
Rwork0.352 3947 -
obs-3947 79 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3SAH.PARAMSAH.TOP
X-RAY DIFFRACTION4SKF_NEW.PARAMSKF.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.231 / Rfactor Rfree: 0.272 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 45 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.45
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.02
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_scbond_it1.772
X-RAY DIFFRACTIONc_mcangle_it2.062
X-RAY DIFFRACTIONc_scangle_it2.652.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.367 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.352

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