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- PDB-3kqv: Crystal Structure of hPNMT in Complex AdoHcy and Formanilide -

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Basic information

Entry
Database: PDB / ID: 3kqv
TitleCrystal Structure of hPNMT in Complex AdoHcy and Formanilide
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
FORMANILIDE / S-ADENOSYL-L-HOMOCYSTEINE / Phenylethanolamine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type

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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)64,7036
Polymers63,6922
Non-polymers1,0114
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint3 kcal/mol
Surface area20190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.379, 94.379, 189.345
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


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-FAN / FORMANILIDE


Mass: 121.137 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.31 Å3/Da / Density % sol: 62.84 %
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: 2.3→50 Å / Num. obs: 38736 / % possible obs: 99.6 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.055 / Χ2: 0.977 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.387.80.28137790.59399.7
2.38-2.487.80.23337950.6299.8
2.48-2.5980.17537890.68399.8
2.59-2.7380.14838540.81899.8
2.73-2.98.20.10838370.874100
2.9-3.128.40.08538481.03199.9
3.12-3.448.60.06438781.16799.9
3.44-3.938.80.05139301.51899.9
3.93-4.959.20.03739401.30899.9
4.95-5090.02540860.9697.2

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Processing

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

1hnn


Resolution: 2.3→18.913 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.822 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1941 5.02 %Random
Rwork0.184 ---
obs0.186 38670 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.616 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 116.61 Å2 / Biso mean: 41.371 Å2 / Biso min: 17.23 Å2
Baniso -1Baniso -2Baniso -3
1-5.048 Å20 Å2-0 Å2
2--5.048 Å2-0 Å2
3----12.105 Å2
Refinement stepCycle: LAST / Resolution: 2.3→18.913 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4099 0 70 315 4484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044280
X-RAY DIFFRACTIONf_angle_d0.8565823
X-RAY DIFFRACTIONf_chiral_restr0.06620
X-RAY DIFFRACTIONf_plane_restr0.009761
X-RAY DIFFRACTIONf_dihedral_angle_d20.9391585
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.3570.2781150.2042550266599
2.357-2.4210.2591440.19425972741100
2.421-2.4920.2341340.17725612695100
2.492-2.5720.2381260.18125912717100
2.572-2.6640.2591320.19125892721100
2.664-2.770.2671460.19525812727100
2.77-2.8960.2671220.20526192741100
2.896-3.0480.2831260.20526342760100
3.048-3.2380.2511570.20525772734100
3.238-3.4870.2321410.19926212762100
3.487-3.8350.2271540.17226202774100
3.835-4.3840.2121520.15426552807100
4.384-5.5010.1721400.14227032843100
5.501-18.9140.1841520.172831298399
Refinement TLS params.Method: refined / Origin x: 24.2719 Å / Origin y: 51.4825 Å / Origin z: -6.1021 Å
111213212223313233
T0.2035 Å2-0.0283 Å2-0.0211 Å2-0.0932 Å20.0357 Å2--0.2152 Å2
L0.4119 °2-0.0544 °2-0.0185 °2-0.3256 °2-0.3259 °2--1.2008 °2
S-0.0531 Å °0.0253 Å °0.0768 Å °0.0649 Å °-0.0093 Å °-0.0161 Å °-0.1488 Å °0.0587 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 - A2003 - 2354

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