[English] 日本語
Yorodumi
- PDB-9hs2: Crystal structure of the Escherichia coli nucleosidase PpnN (ppGp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9hs2
TitleCrystal structure of the Escherichia coli nucleosidase PpnN (ppGpp form)
ComponentsPyrimidine/purine nucleotide 5'-monophosphate nucleosidase
KeywordsHYDROLASE / ppGpp / nucleosidase / GMP
Function / homology
Function and homology information


inosinate nucleosidase activity / pyrimidine-5'-nucleotide nucleosidase activity / pyrimidine-5'-nucleotide nucleosidase / AMP nucleosidase / AMP nucleosidase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / guanosine tetraphosphate binding / protein homotetramerization / protein-containing complex / identical protein binding / cytosol
Similarity search - Function
: / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase, C-terminal domain / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase, N-terminal / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase PpnN-like superfamily / Pyrimidine/purine nucleotide monophosphate nucleosidase, C-terminal / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidases / : / LOG family / Possible lysine decarboxylase
Similarity search - Domain/homology
: / GUANOSINE-5',3'-TETRAPHOSPHATE / Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsBaerentsen, R.L. / Brodersen, D.E.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF17OC0028072 Denmark
Novo Nordisk FoundationNNF17OC0028072 Denmark
CitationJournal: Structure / Year: 2025
Title: Catalytic mechanism and differential alarmone regulation of a conserved stringent nucleosidase
Authors: Baerentsen, R.L. / Kronborg, K. / Brodersen, D.E. / Zhang, Y.E.
History
DepositionDec 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase
B: Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase
C: Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase
D: Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,64310
Polymers206,5054
Non-polymers3,1376
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11700 Å2
ΔGint-25 kcal/mol
Surface area68830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.115, 155.115, 226.088
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

#1: Protein
Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase / AMP nucleosidase / CMP nucleosidase / GMP nucleosidase / IMP nucleosidase / UMP nucleosidase / dTMP ...AMP nucleosidase / CMP nucleosidase / GMP nucleosidase / IMP nucleosidase / UMP nucleosidase / dTMP nucleosidase


Mass: 51626.371 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ppnN, ygdH, b2795, JW2766 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0ADR8, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, pyrimidine-5'-nucleotide nucleosidase, AMP nucleosidase
#2: Chemical
ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N5O17P4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1IXI / 9-deazaguanosine-5'-monophosphate / [(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-4-oxidanyl-5~{H}-pyrrolo[3,2-d]pyrimidin-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate


Mass: 362.233 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C11H15N4O8P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density meas: 203888 Mg/m3 / Density % sol: 63.1 % / Description: octahedral
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 6.6 mg/ml 0.1 M HEPES pH 7.5 4% w/v PEG8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 1.5418 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.4→53.11 Å / Num. obs: 39210 / % possible obs: 99.35 % / Redundancy: 2 % / Biso Wilson estimate: 101.82 Å2 / CC1/2: 0.99 / CC star: 0.99 / Rrim(I) all: 0.09 / Net I/σ(I): 11.11
Reflection shellResolution: 3.4→3.52 Å / Num. unique obs: 3779 / CC1/2: 0.52 / CC star: 0.83 / Rrim(I) all: 1.64 / % possible all: 95.6

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GFM

6gfm


Resolution: 3.4→53.11 Å / SU ML: 0.5552 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.9015
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2832 1916 5 %
Rwork0.2191 36383 -
obs0.2223 38299 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 148.3 Å2
Refinement stepCycle: LAST / Resolution: 3.4→53.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13871 0 192 0 14063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011214337
X-RAY DIFFRACTIONf_angle_d1.469319440
X-RAY DIFFRACTIONf_chiral_restr0.0812154
X-RAY DIFFRACTIONf_plane_restr0.01332533
X-RAY DIFFRACTIONf_dihedral_angle_d8.37221954
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.490.46831200.42882429X-RAY DIFFRACTION93.92
3.49-3.580.39031200.36162557X-RAY DIFFRACTION99.81
3.58-3.690.36551280.33732587X-RAY DIFFRACTION99.74
3.69-3.810.36651520.29832556X-RAY DIFFRACTION99.85
3.81-3.940.33661350.30212563X-RAY DIFFRACTION99.82
3.94-4.10.33161490.26112568X-RAY DIFFRACTION99.74
4.1-4.290.27811330.23582574X-RAY DIFFRACTION99.85
4.29-4.510.30111490.21272567X-RAY DIFFRACTION99.71
4.51-4.80.25271210.19072613X-RAY DIFFRACTION99.89
4.8-5.170.26551460.19962608X-RAY DIFFRACTION99.85
5.17-5.690.30831450.20642612X-RAY DIFFRACTION99.93
5.69-6.510.32151260.21832654X-RAY DIFFRACTION99.89
6.51-8.180.24611330.19862680X-RAY DIFFRACTION99.86
8.19-53.110.21961590.15892815X-RAY DIFFRACTION99.56

+
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