[English] 日本語
Yorodumi
- PDB-5xvq: Crystal structure of monkey Nicotinamide N-methyltransferase (NNM... -

+
Open data


ID or keywords:

Loading...

-
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 / N-methyltransferase activity / methylation / cytosol / cytoplasm
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / 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 / 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 / Glycerol


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more