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- PDB-7rkk: Structure of Nicotinamide N-Methyltransferase (NNMT) in complex w... -

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Basic information

Entry
Database: PDB / ID: 7rkk
TitleStructure of Nicotinamide N-Methyltransferase (NNMT) in complex with II399 (C2 space group)
ComponentsNNMT protein
KeywordsTRANSFERASE/INHIBITOR / Methyltransferase / Inhibitor / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


nicotinamide N-methyltransferase activity / nicotinamide metabolic process / positive regulation of gluconeogenesis / 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. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Chem-5R4 / NNMT protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsYadav, R. / Noinaj, N. / Iyamu, I.D. / Huang, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM117275 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Exploring Unconventional SAM Analogues To Build Cell-Potent Bisubstrate Inhibitors for Nicotinamide N-Methyltransferase.
Authors: Iyamu, I.D. / Vilseck, J.Z. / Yadav, R. / Noinaj, N. / Huang, R.
History
DepositionJul 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NNMT protein
B: NNMT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8964
Polymers62,9322
Non-polymers9642
Water90150
1
A: NNMT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9482
Polymers31,4661
Non-polymers4821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NNMT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9482
Polymers31,4661
Non-polymers4821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.124, 45.676, 101.743
Angle α, β, γ (deg.)90.000, 115.247, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

21A-423-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 6 or (resid 7...
d_2ens_1(chain "B" and (resid 3 through 46 or (resid 47...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERLEUA13 - 270
d_12ens_133B
d_21ens_1SERLEUC1 - 258
d_22ens_133D

NCS oper: (Code: givenMatrix: (-0.0737065701142, 0.0731618716335, 0.994592721701), (0.0460713766967, -0.995990847394, 0.0766789420614), (0.996215222616, 0.0514739977607, 0.0700404010787)Vector: -16. ...NCS oper: (Code: given
Matrix: (-0.0737065701142, 0.0731618716335, 0.994592721701), (0.0460713766967, -0.995990847394, 0.0766789420614), (0.996215222616, 0.0514739977607, 0.0700404010787)
Vector: -16.2613211155, 9.03631674005, 14.0565367982)

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Components

#1: Protein NNMT protein / Nicotinamide N-methyltransferase / isoform CRA_a


Mass: 31466.033 Da / Num. of mol.: 2 / Mutation: K100A, E101A, E103A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NNMT, hCG_39357 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6FH49
#2: Chemical ChemComp-5R4 / 3-[3-(acetyl{[(1R,2R,3S,4R)-4-(4-chloro-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-2,3-dihydroxycyclopentyl]methyl}amino)prop-1-yn-1-yl]benzamide


Mass: 481.931 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H24ClN5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.92 Å3/Da / Density % sol: 36.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium acetate, 0.1 M Tris-HCl, pH 8.5, 30% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.76→50 Å / Num. obs: 11173 / % possible obs: 90.5 % / Redundancy: 5.5 % / Biso Wilson estimate: 36.34 Å2 / CC1/2: 0.938 / CC star: 0.984 / Rpim(I) all: 0.151 / Rrim(I) all: 0.369 / Net I/σ(I): 5.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.5 % / Num. unique obs: 1112 / CC1/2: 0.351 / CC star: 0.721 / % possible all: 91.9

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
HKL-2000data reduction
Cootmodel building
PHASERphasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6PVE

6pve


Resolution: 2.76→46.01 Å / SU ML: 0.4389 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.9719
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2898 1118 10.01 %
Rwork0.2314 10052 -
obs0.2373 11170 88.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.58 Å2
Refinement stepCycle: LAST / Resolution: 2.76→46.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4045 0 68 50 4163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00284207
X-RAY DIFFRACTIONf_angle_d0.60275720
X-RAY DIFFRACTIONf_chiral_restr0.043645
X-RAY DIFFRACTIONf_plane_restr0.0038728
X-RAY DIFFRACTIONf_dihedral_angle_d16.63711504
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.99171088819 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-2.880.39091170.33751044X-RAY DIFFRACTION73.34
2.88-3.030.35881410.29431273X-RAY DIFFRACTION91.58
3.03-3.220.33791440.28271302X-RAY DIFFRACTION91.29
3.22-3.470.31291400.26381265X-RAY DIFFRACTION89.78
3.47-3.820.29071380.22941233X-RAY DIFFRACTION87.49
3.82-4.370.29371400.20121264X-RAY DIFFRACTION89.2
4.37-5.510.23181430.18571287X-RAY DIFFRACTION89.21
5.51-46.010.24881550.19851384X-RAY DIFFRACTION93.16

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