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

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Basic information

Entry
Database: PDB / ID: 7rkl
TitleStructure of Nicotinamide N-Methyltransferase (NNMT) in complex with II399 (P1 space group)
ComponentsNNMT protein
KeywordsTRANSFERASE/INHIBITOR / Methyltransferase / Inhibitor / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


nicotinamide metabolic process / nicotinamide N-methyltransferase activity / positive regulation of protein deacetylation / animal organ regeneration / positive regulation of gluconeogenesis / : / methylation / response to xenobiotic stimulus / 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: 2.08 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
C: NNMT protein
D: NNMT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,36814
Polymers125,8644
Non-polymers2,50410
Water12,070670
1
A: NNMT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1404
Polymers31,4661
Non-polymers6743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NNMT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3326
Polymers31,4661
Non-polymers8665
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 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
4
D: 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)45.676, 62.031, 106.975
Angle α, β, γ (deg.)82.941, 81.924, 68.522
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 4 through 12 or (resid 13...
d_2ens_1(chain "B" and (resid 4 through 12 or (resid 13...
d_3ens_1(chain "C" and (resid 4 through 8 or (resid 9...
d_4ens_1(chain "D" and (resid 4 through 8 or (resid 9...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYPHEA16 - 39
d_12ens_1SERLYSA42 - 150
d_13ens_1ASPLEUA152 - 270
d_21ens_1GLYPHEE13 - 36
d_22ens_1SERLYSE41 - 149
d_23ens_1ASPLEUE151 - 269
d_31ens_1GLYPHEK1 - 24
d_32ens_1SERLYSK27 - 135
d_33ens_1ASPLEUK137 - 255
d_41ens_1GLYLYSM1 - 133
d_42ens_1ASPLEUM135 - 253

NCS oper:
IDCodeMatrixVector
1given(0.999989772655, 0.00203306681344, -0.00403995355744), (0.00202899463153, -0.999997429697, -0.00101182042806), (-0.00404200027207, 0.00100361303574, -0.99999132746)22.8104469662, -21.465029224, -25.368693799
2given(-0.995611125134, -0.0480136964415, 0.0803316404917), (0.0765008372506, 0.0769057841075, 0.994099151127), (-0.0539083426756, 0.995881612103, -0.0728951662673)10.1563005192, 12.7768626526, -45.9939181896
3given(-0.993516306531, -0.0740240405293, 0.0862889916533), (-0.0808127026409, -0.0740358951491, -0.993975851478), (0.0799665914535, -0.994504463365, 0.0675737863237)10.5245297931, 23.4093848911, 20.6114554102

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Components

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


Mass: 31466.033 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: C24H24ClN5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 670 / 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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES, pH 7.0, 2 M ammonium sulfate

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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: 2.08→50 Å / Num. obs: 59068 / % possible obs: 91 % / Redundancy: 3.6 % / Biso Wilson estimate: 23.82 Å2 / CC1/2: 0.975 / CC star: 0.994 / Rpim(I) all: 0.092 / Rrim(I) all: 0.177 / Net I/σ(I): 8.5
Reflection shellResolution: 2.08→2.15 Å / Redundancy: 3.4 % / Num. unique obs: 5457 / CC1/2: 0.583 / CC star: 0.858 / % possible all: 84

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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: 2.08→41.26 Å / SU ML: 0.265 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.2469
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2396 1990 3.37 %
Rwork0.1936 57051 -
obs0.1951 59041 91.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.51 Å2
Refinement stepCycle: LAST / Resolution: 2.08→41.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7994 0 166 670 8830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00378341
X-RAY DIFFRACTIONf_angle_d0.701611346
X-RAY DIFFRACTIONf_chiral_restr0.04661290
X-RAY DIFFRACTIONf_plane_restr0.00531427
X-RAY DIFFRACTIONf_dihedral_angle_d15.10492952
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.380016260506
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.632014998522
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.621731315837
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.130.33161380.27363740X-RAY DIFFRACTION84.19
2.13-2.190.29731340.26054119X-RAY DIFFRACTION92.54
2.19-2.250.31591580.24154099X-RAY DIFFRACTION92.18
2.25-2.330.25751380.23264121X-RAY DIFFRACTION91.91
2.33-2.410.30641400.22584133X-RAY DIFFRACTION91.58
2.41-2.510.29091380.22224033X-RAY DIFFRACTION90.24
2.51-2.620.30141360.21983817X-RAY DIFFRACTION86.25
2.62-2.760.25111350.21343922X-RAY DIFFRACTION88.04
2.76-2.930.27081510.20974259X-RAY DIFFRACTION94.59
2.93-3.160.24751390.19914230X-RAY DIFFRACTION94.46
3.16-3.470.20881460.18044193X-RAY DIFFRACTION92.97
3.47-3.980.19651350.15423886X-RAY DIFFRACTION87.36
3.98-5.010.18571570.1454338X-RAY DIFFRACTION96.63
5.01-41.260.21541450.18264161X-RAY DIFFRACTION93.02

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