[English] 日本語
Yorodumi
- PDB-4wc9: Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodies... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wc9
TitleCatalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation F235L
Components2',3'-cyclic-nucleotide 3'-phosphodiesterase
KeywordsHYDROLASE / myelin / nervous system
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
2',3'-cyclic-nucleotide 3'-phosphodiesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMyllykoski, M. / Raasakka, A. / 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
DepositionSep 4, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2',3'-cyclic-nucleotide 3'-phosphodiesterase


Theoretical massNumber of molelcules
Total (without water)24,2601
Polymers24,2601
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.440, 47.810, 54.170
Angle α, β, γ (deg.)90.000, 94.780, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as asym.

-
Components

#1: Protein 2',3'-cyclic-nucleotide 3'-phosphodiesterase / / CNPase


Mass: 24259.910 Da / Num. of mol.: 1 / Fragment: catalytic domain, residues 179-398 / Mutation: F235L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cnp, Cnp1 / Plasmid: pTH27 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): rosetta
References: UniProt: P16330, 2',3'-cyclic-nucleotide 3'-phosphodiesterase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Na-acetate, PEG4000/6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.223 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.223 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 13840 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 25.69 Å2 / Rmerge F obs: 0.159 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.101 / Χ2: 0.932 / Net I/σ(I): 8.78 / Num. measured all: 44773
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2-2.052.91.0140.6661.91279410109790.80996.9
2.05-2.110.6930.4782.612924103410040.57997.1
2.11-2.170.5390.3743.2528059829530.45397
2.17-2.240.4340.2973.8328869659480.35998.2
2.24-2.310.3810.2474.4726729018800.29997.7
2.31-2.390.3370.2264.8927849088890.27397.9
2.39-2.480.2810.25.6226758458350.2498.8
2.48-2.580.2330.1616.7227128488420.19399.3
2.58-2.70.2010.1377.6226498067970.16498.9
2.7-2.830.1440.1119.1524907507420.13398.9
2.83-2.980.1120.09610.8624967337260.11499
2.98-3.160.0990.08312.2923276766700.09999.1
3.16-3.380.060.06814.9123226726660.0899.1
3.38-3.650.0510.05916.7220505895860.0799.5
3.65-40.0440.05918.0919675605520.0798.6
4-4.470.0410.05618.8917915115040.06798.6
4.47-5.160.0420.05718.5415424484360.06897.3
5.16-6.320.0420.05618.2113073733670.06698.4
6.32-8.940.040.05218.5510413073010.06298
8.940.0370.0519.445391741630.0693.7

-
Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xmi

2xmi


Resolution: 2→27.526 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 31.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2713 691 5 %
Rwork0.2242 13129 -
obs0.2265 13820 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.31 Å2 / Biso mean: 40.3038 Å2 / Biso min: 14.02 Å2
Refinement stepCycle: final / Resolution: 2→27.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1598 0 0 157 1755
Biso mean---34.06 -
Num. residues----206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031665
X-RAY DIFFRACTIONf_angle_d0.682248
X-RAY DIFFRACTIONf_chiral_restr0.026244
X-RAY DIFFRACTIONf_plane_restr0.003287
X-RAY DIFFRACTIONf_dihedral_angle_d12.435620
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0001-2.15440.35631340.28912567270197
2.1544-2.37110.30251370.25552600273798
2.3711-2.7140.28281390.25792632277199
2.714-3.41830.26621390.22422649278899
3.4183-27.52840.24321420.19192681282398
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4380.0353-0.03040.45890.0051.5565-0.04010.02260.0064-0.04830.0379-0.00810.0916-0.113100.18620.0048-0.01170.20420.01780.235740.20258.065619.7031
20.46070.24090.49350.12080.25070.7115-0.01920.0138-0.154-0.00510.0209-0.095-0.06020.1092-00.2316-0.0090.04470.22270.01510.239646.87728.060614.6953
30.74170.5155-0.160.5219-0.38640.5048-0.10780.1372-0.0717-0.20740.1714-0.1204-0.0542-0.137800.3352-0.02550.03250.25430.00820.23740.39216.38458.8209
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 164 through 259 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 260 through 319 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 320 through 378 )A0

+
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