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- PDB-2opb: Structure of K57A hPNMT with inhibitor 3-fluoromethyl-7-thiomorph... -

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Basic information

Entry
Database: PDB / ID: 2opb
TitleStructure of K57A hPNMT with inhibitor 3-fluoromethyl-7-thiomorpholinosulfonamide-THIQ and AdoHcy
ComponentsPhenylethanolamine N-methyltransferase
KeywordsTRANSFERASE / methyltransferase
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-F21 / PHOSPHATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Phenylethanolamine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsDrinkwater, N. / Martin, J.L.
CitationJournal: J.Med.Chem. / Year: 2007
Title: Enzyme Adaptation to Inhibitor Binding: A Cryptic Binding Site in Phenylethanolamine N-Methyltransferase.
Authors: Gee, C.L. / Drinkwater, N. / Tyndall, J.D. / Grunewald, G.L. / Wu, Q. / McLeish, M.J. / Martin, J.L.
History
DepositionJan 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Aug 30, 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 1.3Oct 30, 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)65,1007
Polymers63,5762
Non-polymers1,5255
Water1,31573
1
A: Phenylethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5033
Polymers31,7881
Non-polymers7152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Phenylethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5984
Polymers31,7881
Non-polymers8103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-19 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.420, 94.420, 187.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Detailsthe biological unit is a monomer

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Components

#1: Protein Phenylethanolamine N-methyltransferase / PNMTase / Noradrenaline N-methyltransferase


Mass: 31787.865 Da / Num. of mol.: 2 / Mutation: K57A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PNMT, PENT / Plasmid: PNMT-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P11086, phenylethanolamine N-methyltransferase
#2: Chemical ChemComp-F21 / (3R)-3-(FLUOROMETHYL)-7-(THIOMORPHOLIN-4-YLSULFONYL)-1,2,3,4-TETRAHYDROISOQUINOLINE / 3-FLUOROMETHYL 7-THIOMORPHOLINOSULFONAMIDE 1,2,3,4-TETRAHYDROISOQUINOLINE


Mass: 330.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H19FN2O2S2
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 3.29 Å3/Da / Density % sol: 62.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 8% PEG6K, 0.25 M LiCl, 0.1 M cacodylate, pH 5.8, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 22, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1HiRes2SINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→66.77 Å / Num. obs: 21616 / % possible obs: 99.8 % / Redundancy: 7.06 % / Rmerge(I) obs: 0.114 / Χ2: 0.89 / Net I/σ(I): 7.7 / Scaling rejects: 1155
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.8-2.97.250.52821519920960.64100
2.9-3.027.280.4692.21544021220.69100
3.02-3.157.280.3992.41547221260.68100
3.15-3.327.30.33831550621230.8100
3.32-3.537.150.2524.21530521400.89100
3.53-3.86.980.18661492921330.99100
3.8-4.186.940.1278.81509021610.97100
4.18-4.796.910.111.91529521930.9699.8
4.79-6.036.980.09113.71552721950.8899.9
6.03-66.776.640.066231610223271.4598.9

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata processing
CNS1.1refinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 1HNN

1hnn


Resolution: 2.8→54.4 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 647660.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1034 4.9 %RANDOM
Rwork0.236 ---
obs-20914 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.248 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso mean: 76.2 Å2
Baniso -1Baniso -2Baniso -3
1-12.08 Å20 Å20 Å2
2--12.08 Å20 Å2
3----24.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.8→54.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4091 0 99 73 4263
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.421 158 4.6 %
Rwork0.356 3261 -
obs-3419 97.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2farII210.parfarII210.top
X-RAY DIFFRACTION3sah.parsah.top
X-RAY DIFFRACTION4water_rep.paramwater.top
X-RAY DIFFRACTION5ion.paramion.top
X-RAY DIFFRACTION6
X-RAY DIFFRACTION7
X-RAY DIFFRACTION8
X-RAY DIFFRACTION9
X-RAY DIFFRACTION10

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