[English] 日本語
Yorodumi
- PDB-8r17: Crystal structure of Neurospora crassa NADase with modified C-terminus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8r17
TitleCrystal structure of Neurospora crassa NADase with modified C-terminus
ComponentsConidial surface nicotinamide adenine dinucleotide glycohydrolase,Conidial surface nicotinamide adenine dinucleotide glycohydrolase nadA
KeywordsHYDROLASE / NADase / NAD hydrolase / homodimer / glycoprotein / extracellular / TNT domain
Function / homology
Function and homology information


NAD+ glycohydrolase / NADP+ nucleosidase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / extracellular region / metal ion binding
Similarity search - Function
: / Tuberculosis necrotizing toxin / Tuberculosis necrotizing toxin
Similarity search - Domain/homology
Conidial surface nicotinamide adenine dinucleotide glycohydrolase nadA / Conidial surface nicotinamide adenine dinucleotide glycohydrolase
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKallio, J.P. / Ferrario, E. / Ziegler, M.
Funding support Norway, 1items
OrganizationGrant numberCountry
Norwegian Research Council302314 Norway
CitationJournal: Protein Sci. / Year: 2024
Title: Evolution of fungal tuberculosis necrotizing toxin (TNT) domain-containing enzymes reveals divergent adaptations to enhance NAD cleavage.
Authors: Ferrario, E. / Kallio, J.P. / Emdadi, M. / Stromland, O. / Rack, J.G.M. / Ziegler, M.
History
DepositionNov 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Conidial surface nicotinamide adenine dinucleotide glycohydrolase,Conidial surface nicotinamide adenine dinucleotide glycohydrolase nadA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2346
Polymers28,1831
Non-polymers1,0515
Water41423
1
A: Conidial surface nicotinamide adenine dinucleotide glycohydrolase,Conidial surface nicotinamide adenine dinucleotide glycohydrolase nadA
hetero molecules

A: Conidial surface nicotinamide adenine dinucleotide glycohydrolase,Conidial surface nicotinamide adenine dinucleotide glycohydrolase nadA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,46912
Polymers56,3672
Non-polymers2,10210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area5590 Å2
ΔGint-9 kcal/mol
Surface area19950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.756, 83.756, 103.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-303-

GOL

-
Components

#1: Protein Conidial surface nicotinamide adenine dinucleotide glycohydrolase,Conidial surface nicotinamide adenine dinucleotide glycohydrolase nadA / NAD(P)ase / NADase / Diphosphopyridine nucleotidase / DPNase / NAD(+) hydrolase / NADP(+) hydrolase ...NAD(P)ase / NADase / Diphosphopyridine nucleotidase / DPNase / NAD(+) hydrolase / NADP(+) hydrolase / NADase / NAD(+) hydrolase nadA / NADP(+) hydrolase nadA


Mass: 28183.324 Da / Num. of mol.: 1
Mutation: 233-EDPQRLVPRNY-243 replaced by LDESEYDEKVEYSNPYTPGPNQ
Source method: isolated from a genetically manipulated source
Details: MKFTLLSTAVALLTSTAVA = signal sequence DVLFQGPGHHHHHH = 3C proteace cleavage site and HIS-tag 233-DESEYDEKVEYSNPYTPGPNQ-254 = engineered modification, sequence from AfNADase C- ...Details: MKFTLLSTAVALLTSTAVA = signal sequence DVLFQGPGHHHHHH = 3C proteace cleavage site and HIS-tag 233-DESEYDEKVEYSNPYTPGPNQ-254 = engineered modification, sequence from AfNADase C-terminus,MKFTLLSTAVALLTSTAVA = signal sequence DVLFQGPGHHHHHH = 3C proteace cleavage site and HIS-tag 233-DESEYDEKVEYSNPYTPGPNQ-254 = engineered modification, sequence from AfNADase C-terminus
Source: (gene. exp.) Neurospora crassa (fungus), (gene. exp.) Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293 (mold)
Gene: NCU07948, nadA, AFUA_6G14470 / Strain: ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q7S936, UniProt: Q4WL81, NAD+ glycohydrolase, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#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.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: Bis-Tris pH 5.5-6.5, NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.3→43.98 Å / Num. obs: 16949 / % possible obs: 100 % / Redundancy: 8.6 % / Biso Wilson estimate: 75.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.018 / Net I/σ(I): 20.1
Reflection shellResolution: 2.3→2.38 Å / % possible obs: 99.9 % / Rmerge(I) obs: 1.828 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1626 / CC1/2: 0.442 / Rpim(I) all: 0.666

-
Processing

Software
NameVersionClassification
PHENIX1.21rc1_5109refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→43.94 Å / SU ML: 0.3524 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.6736
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2578 867 5.13 %
Rwork0.2336 16031 -
obs0.2349 16898 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.14 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1463 0 68 23 1554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00521579
X-RAY DIFFRACTIONf_angle_d0.75762157
X-RAY DIFFRACTIONf_chiral_restr0.0477233
X-RAY DIFFRACTIONf_plane_restr0.0067277
X-RAY DIFFRACTIONf_dihedral_angle_d14.0296530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.440.36281460.33732594X-RAY DIFFRACTION99.93
2.44-2.630.3991540.34882615X-RAY DIFFRACTION100
2.63-2.90.36991450.31452638X-RAY DIFFRACTION100
2.9-3.320.37131380.31012655X-RAY DIFFRACTION99.96
3.32-4.180.23971380.22322689X-RAY DIFFRACTION99.96
4.18-43.940.21251460.19742840X-RAY DIFFRACTION99.7

+
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