[English] 日本語
Yorodumi
- PDB-5ae0: Perdeuterated mouse CNPase catalytic domain at atomic resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ae0
TitlePerdeuterated mouse CNPase catalytic domain at atomic resolution
Components2', 3'-CYCLIC-NUCLEOTIDE 3'-PHOSPHODIESTERASE
KeywordsHYDROLASE
Function / homology
Function and homology information


cyclic nucleotide catabolic process / 2',3'-cyclic-nucleotide 3'-phosphodiesterase / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / myelin sheath adaxonal region / myelin sheath abaxonal region / cyclic nucleotide binding / regulation of mitochondrial membrane permeability / oligodendrocyte differentiation / pseudopodium / microvillus ...cyclic nucleotide catabolic process / 2',3'-cyclic-nucleotide 3'-phosphodiesterase / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / myelin sheath adaxonal region / myelin sheath abaxonal region / cyclic nucleotide binding / regulation of mitochondrial membrane permeability / oligodendrocyte differentiation / pseudopodium / microvillus / forebrain development / axonogenesis / adult locomotory behavior / cell projection / response to toxic substance / melanosome / myelin sheath / mitochondrial inner membrane / microtubule / mitochondrial outer membrane / response to lipopolysaccharide / perinuclear region of cytoplasm / extracellular space / RNA binding / membrane / cytoplasm
Similarity search - Function
: / 2',3'-cyclic nucleotide 3'-phosphodiesterase fold / 2',3'-cyclic nucleotide 3'-phosphodiesterase superfamily / Cyclic nucleotide phosphodiesterase / 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP or CNPase) / Cyclic phosphodiesterase / AAA domain / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / 2',3'-cyclic-nucleotide 3'-phosphodiesterase
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å
AuthorsLaulumaa, S. / Kursula, P.
CitationJournal: Sci Rep / Year: 2015
Title: Determinants of ligand binding and catalytic activity in the myelin enzyme 2',3'-cyclic nucleotide 3'-phosphodiesterase.
Authors: Raasakka, A. / Myllykoski, M. / Laulumaa, S. / Lehtimaki, M. / Hartlein, M. / Moulin, M. / Kursula, I. / Kursula, P.
History
DepositionAug 25, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jan 30, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Experimental preparation
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / exptl_crystal_grow
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: 2', 3'-CYCLIC-NUCLEOTIDE 3'-PHOSPHODIESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5223
Polymers24,2941
Non-polymers2282
Water5,080282
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.650, 47.560, 51.220
Angle α, β, γ (deg.)90.00, 97.51, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein 2', 3'-CYCLIC-NUCLEOTIDE 3'-PHOSPHODIESTERASE / CNP / CNPASE


Mass: 24293.928 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, UNP RESIDUES 179-398
Source method: isolated from a genetically manipulated source
Details: PERDEUTERATED / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PETNKI-HIS3C-LIC-KAN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA
References: UniProt: P16330, 2',3'-cyclic-nucleotide 3'-phosphodiesterase
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 1.97 Å3/Da / Density % sol: 37.59 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 3.5 / Details: 25% PEG3350, 50 MM ACETATE, PD 3.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.913
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.913 Å / Relative weight: 1
ReflectionResolution: 1.04→30 Å / Num. obs: 90347 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 8.77 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.6
Reflection shellResolution: 1.04→1.07 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.26 / Mean I/σ(I) obs: 1.1 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WUT

2wut


Resolution: 1.04→29.287 Å / SU ML: 0.1 / σ(F): 1.99 / Phase error: 17.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1563 1807 2 %
Rwork0.127 --
obs0.1276 90320 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.04→29.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1688 0 14 282 1984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192200
X-RAY DIFFRACTIONf_angle_d1.6183028
X-RAY DIFFRACTIONf_dihedral_angle_d16.639854
X-RAY DIFFRACTIONf_chiral_restr0.384307
X-RAY DIFFRACTIONf_plane_restr0.011414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.04-1.06810.31941370.28946730X-RAY DIFFRACTION99
1.0681-1.09950.27371380.24486743X-RAY DIFFRACTION99
1.0995-1.1350.24191380.20196758X-RAY DIFFRACTION100
1.135-1.17560.22251380.16416780X-RAY DIFFRACTION100
1.1756-1.22270.17671390.14586802X-RAY DIFFRACTION100
1.2227-1.27830.17461390.13446807X-RAY DIFFRACTION100
1.2783-1.34570.16231390.12016812X-RAY DIFFRACTION100
1.3457-1.430.16291390.10816803X-RAY DIFFRACTION100
1.43-1.54040.15821390.09346806X-RAY DIFFRACTION100
1.5404-1.69540.11661380.08016805X-RAY DIFFRACTION100
1.6954-1.94070.11571400.08646849X-RAY DIFFRACTION100
1.9407-2.44490.11111400.10686853X-RAY DIFFRACTION100
2.4449-29.2990.15221430.12846965X-RAY DIFFRACTION100

+
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