[English] 日本語
Yorodumi
- PDB-1kqn: Crystal structure of NMN/NaMN adenylyltransferase complexed with NAD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kqn
TitleCrystal structure of NMN/NaMN adenylyltransferase complexed with NAD
ComponentsNICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE
KeywordsTRANSFERASE / nucleotidyltransferase superfamily
Function / homology
Function and homology information


negative regulation of apoptotic DNA fragmentation / protein ADP-ribosyltransferase-substrate adaptor activity / nicotinamide-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / nicotinate-nucleotide adenylyltransferase / nucleotide biosynthetic process / nicotinate-nucleotide adenylyltransferase activity / Nicotinate metabolism / ATP generation from poly-ADP-D-ribose / NAD+ biosynthetic process ...negative regulation of apoptotic DNA fragmentation / protein ADP-ribosyltransferase-substrate adaptor activity / nicotinamide-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / nicotinate-nucleotide adenylyltransferase / nucleotide biosynthetic process / nicotinate-nucleotide adenylyltransferase activity / Nicotinate metabolism / ATP generation from poly-ADP-D-ribose / NAD+ biosynthetic process / neuron projection maintenance / response to wounding / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / nuclear body / negative regulation of DNA-templated transcription / chromatin / nucleoplasm / ATP binding / identical protein binding / nucleus
Similarity search - Function
Nicotinamide/nicotinate mononucleotide adenylyltransferase, eukaryotic / : / Nicotinate/nicotinamide nucleotide adenylyltransferase / Cytidylyltransferase-like / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / XENON / Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsZhou, T. / Kurnasov, O. / Tomchick, D.R. / Binns, D.D. / Grishin, N.V. / Marquez, V.E. / Osterman, A.L. / Zhang, H.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structure of Human Nicotinamide/Nicotonic Acid Mononucleotide Adenylyltransferase. Basis for the dual substrate specificity and activation of the oncolytic agent tiazofurin.
Authors: Zhou, T. / Kurnasov, O. / Tomchick, D.R. / Binns, D.D. / Grishin, N.V. / Marquez, V.E. / Osterman, A.L. / Zhang, H.
History
DepositionJan 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE
B: NICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE
C: NICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE
D: NICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE
E: NICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE
F: NICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,84527
Polymers191,8956
Non-polymers5,95021
Water11,295627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.816, 90.879, 136.585
Angle α, β, γ (deg.)90.00, 116.85, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is hexamer, containing chains A, B, C, D, E, F, in the asymmetric unit.

-
Components

#1: Protein
NICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE / NMNAT


Mass: 31982.502 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HAN9, nicotinamide-nucleotide adenylyltransferase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Xe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / 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: 3.77 Å3/Da / Density % sol: 67.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Na Formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mg/mlprotein1drop
2100 mMHEPES1droppH7.2
30.5 M1dropNaCl
42 mMdithiothreitol1drop
51 mMEDTA1drop
60.03 %Brij-351drop
710 mMNAD1drop
80.1 Msodium acetate1reservoirpH4.2-4.6
91.6-1.8 Msodium formate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 20, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 132989 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.28 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 12.9
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 1.9 / % possible all: 84.8
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. measured all: 435916 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 84.8 % / Mean I/σ(I) obs: 1.9

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 6364 5 %RANDOM
Rwork0.218 ---
all-145100 --
obs-125457 86.5 %-
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11176 0 279 627 12082
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.25 / Highest resolution: 2.2 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.014
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.6

+
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