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- PDB-5xvq: Crystal structure of monkey Nicotinamide N-methyltransferase (NNM... -

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Basic information

Entry
Database: PDB / ID: 5xvq
TitleCrystal structure of monkey Nicotinamide N-methyltransferase (NNMT) bound with end product, 1-methyl Nicotinamide (MNA)
ComponentsNicotinamide N-methyltransferase (NNMT)
KeywordsTRANSFERASE / NNMT / MNA / ternary complex / feedback inhibition / T2D
Function / homology
Function and homology information


nicotinamide N-methyltransferase activity / nicotinamide metabolic process / positive regulation of protein deacetylation / 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. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-carbamoyl-1-methylpyridin-1-ium / S-ADENOSYL-L-HOMOCYSTEINE / Nicotinamide N-methyltransferase
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsBirudukota, S. / Swaminathan, S. / Thakur, M.K. / Parveen, R. / Kandan, S. / Kannt, A. / Gosu, R.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Crystal structures of monkey and mouse nicotinamide N-methyltransferase (NNMT) bound with end product, 1-methyl nicotinamide
Authors: Swaminathan, S. / Birudukota, S. / Thakur, M.K. / Parveen, R. / Kandan, S. / Juluri, S. / Shaik, S. / Anand, N.N. / Burri, R.R. / Kristam, R. / Hallur, M.S. / Rajagopal, S. / Schreuder, H. / ...Authors: Swaminathan, S. / Birudukota, S. / Thakur, M.K. / Parveen, R. / Kandan, S. / Juluri, S. / Shaik, S. / Anand, N.N. / Burri, R.R. / Kristam, R. / Hallur, M.S. / Rajagopal, S. / Schreuder, H. / Langer, T. / Rudolph, C. / Ruf, S. / Dhakshinamoorthy, S. / Gosu, R. / Kannt, A.
History
DepositionJun 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.formula / _chem_comp.name ..._chem_comp.formula / _chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nicotinamide N-methyltransferase (NNMT)
B: Nicotinamide N-methyltransferase (NNMT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0728
Polymers63,8452
Non-polymers1,2276
Water3,459192
1
A: Nicotinamide N-methyltransferase (NNMT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5364
Polymers31,9221
Non-polymers6143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint0 kcal/mol
Surface area10630 Å2
MethodPISA
2
B: Nicotinamide N-methyltransferase (NNMT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5364
Polymers31,9221
Non-polymers6143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-1 kcal/mol
Surface area10710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.071, 65.028, 91.144
Angle α, β, γ (deg.)90.000, 89.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nicotinamide N-methyltransferase (NNMT) / Uncharacterized protein


Mass: 31922.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: NNMT, EGK_06915 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F7ERX8
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-8GC / 3-carbamoyl-1-methylpyridin-1-ium / 1-methylnicotinamide


Mass: 137.159 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H9N2O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

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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: 1.95 Å3/Da / Density % sol: 37.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 0.1M MES pH 6.2, 23%(w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 18, 2017 / Details: VariMax HR Optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.29→91.29 Å / Num. obs: 21145 / % possible obs: 95.4 % / Redundancy: 4 % / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.096 / Rrim(I) all: 0.202 / Χ2: 1.069 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.382.30.5110.6470.3810.6421.0883.4
2.38-2.482.80.50.7190.3340.6051.0390.9
2.48-2.593.40.4540.7730.2770.5351.08496.3
2.59-2.734.10.4220.8080.2330.4841.09796.3
2.73-2.94.40.3520.8920.1870.41.05897.1
2.9-3.124.50.2570.9360.1330.2911.06597.1
3.12-3.444.50.2010.9630.1050.2281.03597.7
3.44-3.934.50.1470.9660.0780.1671.08398.3
3.93-4.954.50.1170.9820.0610.1321.06298.6
2.29-2.384.40.1080.9860.0560.1231.08998.1

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Processing

Software
NameVersionClassification
HKL-2000706data scaling
REFMAC5.2.0005refinement
PDB_EXTRACT3.22data extraction
HKL-2000706data reduction
MOLREP8.2.01phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ROD

3rod


Resolution: 2.29→91.29 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.896 / SU B: 9.138 / SU ML: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.588 / ESU R Free: 0.289 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2615 1085 5.1 %RANDOM
Rwork0.1938 ---
obs0.1972 20046 95.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 43.07 Å2 / Biso mean: 25.205 Å2 / Biso min: 13.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å2-0.2 Å2
2---0.46 Å20 Å2
3---1.45 Å2
Refinement stepCycle: final / Resolution: 2.29→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3986 0 84 192 4262
Biso mean--21.96 26.8 -
Num. residues----504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224248
X-RAY DIFFRACTIONr_angle_refined_deg1.2492.0145757
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2615523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18124.565184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.08515770
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3571523
X-RAY DIFFRACTIONr_chiral_restr0.0830.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023189
X-RAY DIFFRACTIONr_nbd_refined0.1950.21955
X-RAY DIFFRACTIONr_nbtor_refined0.30.22862
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2238
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.215
LS refinement shellResolution: 2.293→2.353 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 63 -
Rwork0.274 1204 -
all-1267 -
obs--77.3 %

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