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- PDB-3kqw: Crystal Structure of hPNMT in Complex AdoHcy and 5-Chlorobenzimidazole -

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Basic information

Entry
Database: PDB / ID: 3kqw
TitleCrystal Structure of hPNMT in Complex AdoHcy and 5-Chlorobenzimidazole
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
5-chloro-1H-benzimidazole / S-ADENOSYL-L-HOMOCYSTEINE / Phenylethanolamine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.486 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 27, 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)64,7666
Polymers63,6922
Non-polymers1,0744
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-13 kcal/mol
Surface area20820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.405, 94.405, 189.535
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-ES9 / 5-chloro-1H-benzimidazole


Mass: 152.581 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5ClN2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 3.32 Å3/Da / Density % sol: 62.9 %
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: 2.5→50 Å / Num. obs: 28974 / % possible obs: 93.6 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.143 / Χ2: 1.384 / Net I/σ(I): 6.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.593.50.58518860.49762.5
2.59-2.694.30.60223730.52378.9
2.69-2.825.20.55629280.60196.5
2.82-2.966.80.51730440.673100
2.96-3.1580.42330470.746100
3.15-3.398.50.29730950.945100
3.39-3.738.60.18730791.373100
3.73-4.278.60.13230971.884100
4.27-5.388.70.09931672.226100
5.38-508.40.06732582.42196.9

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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: 2.486→19.32 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.72 / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1501 5.2 %Random
Rwork0.194 ---
obs0.197 28844 93.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.428 Å2 / ksol: 0.317 e/Å3
Displacement parametersBiso max: 141.92 Å2 / Biso mean: 56.216 Å2 / Biso min: 21.77 Å2
Baniso -1Baniso -2Baniso -3
1-7.147 Å20 Å2-0 Å2
2--7.147 Å2-0 Å2
3----14.293 Å2
Refinement stepCycle: LAST / Resolution: 2.486→19.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4099 0 72 155 4326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084284
X-RAY DIFFRACTIONf_angle_d1.1345833
X-RAY DIFFRACTIONf_chiral_restr0.075620
X-RAY DIFFRACTIONf_plane_restr0.005759
X-RAY DIFFRACTIONf_dihedral_angle_d21.1131581
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.486-2.5660.415750.3491496157157
2.566-2.6580.3871300.2941959208976
2.658-2.7640.3561420.2762443258593
2.764-2.8890.4041240.25626242748100
2.889-3.0410.3111250.24226552780100
3.041-3.230.3181510.23926062757100
3.23-3.4790.3081450.22226592804100
3.479-3.8260.2431570.1826492806100
3.826-4.3740.2331570.15626692826100
4.374-5.490.1991420.13427212863100
5.49-19.320.1911530.15128623015100
Refinement TLS params.Method: refined / Origin x: 24.1503 Å / Origin y: 51.3773 Å / Origin z: -5.8547 Å
111213212223313233
T0.3031 Å2-0.0397 Å2-0.0278 Å2-0.1969 Å20.0444 Å2--0.334 Å2
L0.5256 °2-0.091 °20.0048 °2-0.3799 °2-0.307 °2--1.3208 °2
S-0.0524 Å °0.0079 Å °0.0658 Å °0.0806 Å °-0.0075 Å °-0.0116 Å °-0.1322 Å °0.0013 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 - A2005 - 2186

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