[English] 日本語
Yorodumi
- PDB-1gzu: Crystal Structure of Human Nicotinamide Mononucleotide Adenylyltr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gzu
TitleCrystal Structure of Human Nicotinamide Mononucleotide Adenylyltransferase in Complex with NMN
ComponentsNICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE
KeywordsTRANSFERASE / NAD BIOSYNTHESIS / ADENYLYLTRANSFERASE
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 / 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
BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsWerner, E. / Ziegler, M. / Lerner, F. / Schweiger, M. / Heinemann, U.
CitationJournal: FEBS Lett. / Year: 2002
Title: Crystal structure of human nicotinamide mononucleotide adenylyltransferase in complex with NMN.
Authors: Werner, E. / Ziegler, M. / Lerner, F. / Schweiger, M. / Heinemann, U.
History
SupersessionJun 6, 2002ID: 1GRY
DepositionJun 6, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 13, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: citation / diffrn_radiation ...citation / diffrn_radiation / diffrn_source / pdbx_unobs_or_zero_occ_atoms / refine / struct
Item: _citation.page_last / _citation.title ..._citation.page_last / _citation.title / _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_source.pdbx_wavelength_list / _refine.pdbx_method_to_determine_struct / _struct.title

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,3396
Polymers100,3333
Non-polymers1,0063
Water00
1
A: NICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE
B: NICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE
C: NICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE
hetero molecules

A: NICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE
B: NICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE
C: NICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,67812
Polymers200,6666
Non-polymers2,0116
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)140.800, 235.700, 89.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A6 - 270
2113B6 - 270
3113C6 - 270

NCS oper:
IDCodeMatrixVector
1given(-0.4551, 0.8629, -0.2197), (-0.8654, -0.4867, -0.119), (-0.2096, 0.136, 0.9683)-62.16, 118.3, -9.598
2given(-0.493, -0.8439, -0.2118), (0.8501, -0.519, 0.0895), (-0.1855, -0.1359, 0.9732)69.53, 116.2, 11.45

-
Components

#1: Protein NICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE / NMN ADENYLYLTRANSFERASE


Mass: 33444.406 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): NM522
References: UniProt: Q9HAN9, nicotinamide-nucleotide adenylyltransferase
#2: Chemical ChemComp-NMN / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / NICOTINAMIDE MONONUCLEOTIDE


Mass: 335.227 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H16N2O8P
Sequence detailsN-TERMINUS INCLUDES A HIS-TAG

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.71 Å3/Da / Density % sol: 66.56 %
Crystal growpH: 7.5
Details: 2.0 M NA/KH2PO4, 100 M M TRIS PH 7.5, 5% 2-PROPANOL
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Werner, E., (2002) Acta Crystallogr., D58, 140.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 mg/mlprotein1drop
270 mMammonium sulfate1drop
3100 mMimidazole1drop
4300 mM1dropNaCl
51 mM1dropMgCl2
62.5 mMdithiothreitol1drop
71 mMNAD+1drop
81.9 Msodium potassium phosphate1reservoir
90.1 MTris-HCl1reservoirpH7.5
105 %2-propanol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 / Wavelength: 0.9795 Å
DetectorDetector: CCD / Date: Jun 17, 2001 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 62691 / % possible obs: 98.3 % / Observed criterion σ(I): 0.5 / Redundancy: 10.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.2
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 1.1 / % possible all: 92.5
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 632186 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 92.5 % / Num. unique obs: 5937

-
Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.85 / SU B: 8.754 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.801 / ESU R Free: 0.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1438 5 %RANDOM
Rwork0.246 ---
obs0.248 27097 86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5478 0 66 0 5544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0215632
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.9597636
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3053675
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.177151042
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1330.2870
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024128
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3350.33116
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.5409
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.374
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3810.53
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.79823386
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.96885473
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.71842246
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.757122163
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A907tight positional0.060.05
2B907tight positional0.060.05
3C907tight positional0.060.05
1A896loose positional0.685
2B896loose positional0.545
3C896loose positional0.595
1A907tight thermal0.160.5
2B907tight thermal0.130.5
3C907tight thermal0.20.5
1A896loose thermal5.5910
2B896loose thermal4.3310
3C896loose thermal6.9710
LS refinement shellResolution: 2.9→2.97 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.342 71
Rwork0.266 1308
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 20 Å / % reflection Rfree: 7 % / Rfactor Rfree: 0.291 / Rfactor Rwork: 0.253
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.719

+
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://pdbjlvh1.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