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- PDB-3kqt: Crystal Structure of hPNMT in Complex AdoHcy and 2-Amino-1-methyl... -

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Basic information

Entry
Database: PDB / ID: 3kqt
TitleCrystal Structure of hPNMT in Complex AdoHcy and 2-Amino-1-methylbenzimidazole
ComponentsPhenylethanolamine N-methyltransferase
KeywordsTRANSFERASE / methyltransferase / fragment screening / Catecholamine biosynthesis / 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
1-methyl-1H-benzimidazol-2-amine / S-ADENOSYL-L-HOMOCYSTEINE / Phenylethanolamine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.399 Å
AuthorsDrinkwater, N. / Martin, J.L.
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
DepositionNov 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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)64,7556
Polymers63,6922
Non-polymers1,0634
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-13 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.852, 93.852, 188.503
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-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-ES7 / 1-methyl-1H-benzimidazol-2-amine


Mass: 147.177 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H9N3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 3.26 Å3/Da / Density % sol: 62.25 %
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: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95667 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 30, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95667 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 33746 / % possible obs: 99.7 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.077 / Χ2: 1.036 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.498.30.54633010.50799.8
2.49-2.599.30.41733180.522100
2.59-2.79.70.32633140.552100
2.7-2.859.80.23633470.61100
2.85-3.029.80.16133350.715100
3.02-3.269.80.11933480.868100
3.26-3.589.70.08233741.234100
3.58-4.19.60.06333921.71199.9
4.1-5.179.50.0534501.88299.9
5.17-508.80.03635671.65597.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
MIFitphasing
RefinementStarting model: PDB entry 1HNN

1hnn


Resolution: 2.399→19.486 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.821 / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1714 5.09 %Random
Rwork0.181 ---
obs0.184 33678 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.945 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso max: 132.66 Å2 / Biso mean: 47.986 Å2 / Biso min: 19.7 Å2
Baniso -1Baniso -2Baniso -3
1-5.801 Å20 Å2-0 Å2
2--5.801 Å2-0 Å2
3----11.602 Å2
Refinement stepCycle: LAST / Resolution: 2.399→19.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4099 0 74 277 4450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064286
X-RAY DIFFRACTIONf_angle_d0.9535837
X-RAY DIFFRACTIONf_chiral_restr0.064620
X-RAY DIFFRACTIONf_plane_restr0.004759
X-RAY DIFFRACTIONf_dihedral_angle_d20.7461581
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.399-2.4690.3141270.2072602272999
2.469-2.5490.2681430.19426072750100
2.549-2.640.2671470.19425992746100
2.64-2.7450.261390.226352774100
2.745-2.870.3311250.20326372762100
2.87-3.020.2631250.20726602785100
3.02-3.2090.2691510.21626322783100
3.209-3.4550.2671470.19626582805100
3.455-3.8010.2331580.17726582816100
3.801-4.3450.2221560.15426712827100
4.345-5.4550.1721430.13827342877100
5.455-19.4870.1771530.15428713024100
Refinement TLS params.Method: refined / Origin x: 23.9574 Å / Origin y: 51.0101 Å / Origin z: -5.9121 Å
111213212223313233
T0.2365 Å2-0.032 Å2-0.019 Å2-0.1503 Å20.0611 Å2--0.2675 Å2
L0.4284 °2-0.0353 °20.0046 °2-0.41 °2-0.33 °2--1.4488 °2
S-0.0657 Å °0.0312 Å °0.0975 Å °0.0952 Å °-0.017 Å °-0.0323 Å °-0.1092 Å °0.0457 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA24 - 280
2X-RAY DIFFRACTION1allB14 - 281
3X-RAY DIFFRACTION1allA - B2001 - 2002
4X-RAY DIFFRACTION1allA - B1 - 290
5X-RAY DIFFRACTION1allB - A2006 - 2319

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