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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wdh
TitleCatalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation Y168A
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 / oligodendrocyte differentiation / axonogenesis / adult locomotory behavior / response to toxic substance / melanosome / myelin sheath / extracellular space ...cyclic nucleotide catabolic process / 2',3'-cyclic-nucleotide 3'-phosphodiesterase / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / oligodendrocyte differentiation / axonogenesis / adult locomotory behavior / response to toxic substance / melanosome / myelin sheath / 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
ACETIC ACID / 2',3'-cyclic-nucleotide 3'-phosphodiesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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 8, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 30, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3334
Polymers24,2021
Non-polymers1313
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-16 kcal/mol
Surface area11540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.310, 48.330, 54.030
Angle α, β, γ (deg.)90.000, 94.520, 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: 24201.830 Da / Num. of mol.: 1 / Fragment: catalytic domain, residues 179-398 / Mutation: Y168A
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: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.11 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Na-acetate, PEG 4000 / 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 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.223 Å / Relative weight: 1
ReflectionResolution: 1.9→60 Å / Num. obs: 14974 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 23.65 Å2 / Rmerge F obs: 0.15 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.083 / Χ2: 0.982 / Net I/σ(I): 9.49 / Num. measured all: 42879
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.9-1.951.81.3060.7221.27155511758500.92772.3
1.95-20.9750.581.692203117110050.72385.8
2-2.060.750.472.22234611169960.58189.2
2.06-2.120.4590.3323.12229510699590.40989.7
2.12-2.190.3960.2683.67239610699650.3390.3
2.19-2.270.3480.234.45237810049210.28491.7
2.27-2.360.3340.24.8324329979250.24792.8
2.36-2.450.2790.1745.5924789519070.21395.4
2.45-2.560.2570.1646.3325049048740.296.7
2.56-2.690.2110.137.8825398858590.15897.1
2.69-2.830.1510.1029.6225438368200.12398.1
2.83-30.1140.08911.6525247817760.10799.4
3-3.210.0730.0715.0925317397380.08399.9
3.21-3.470.0450.05519.8624446896830.06599.1
3.47-3.80.0410.0521.5522836336300.05999.5
3.8-4.250.0380.05123.7421145815790.0699.7
4.25-4.910.0350.04923.7818435185160.05799.6
4.91-6.010.0320.04323.3815614344310.0599.3
6.01-8.50.0290.03724.0512253423400.04399.4
8.50.0240.03425.696852022000.0499

-
Phasing

PhasingMethod: molecular replacement

-
Processing

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

2xmi


Resolution: 1.9→53.862 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 30.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2592 748 5 %
Rwork0.2168 14204 -
obs0.2189 14952 93.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.25 Å2 / Biso mean: 43.8576 Å2 / Biso min: 13.57 Å2
Refinement stepCycle: final / Resolution: 1.9→53.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1658 0 9 153 1820
Biso mean--44.14 37.43 -
Num. residues----213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031720
X-RAY DIFFRACTIONf_angle_d0.7142318
X-RAY DIFFRACTIONf_chiral_restr0.027250
X-RAY DIFFRACTIONf_plane_restr0.004297
X-RAY DIFFRACTIONf_dihedral_angle_d14.376645
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 (%)
1.9003-2.0470.3781300.31912460259082
2.047-2.2530.32051440.26962743288790
2.253-2.5790.30721530.25912895304895
2.579-3.24920.28731580.23353007316599
3.2492-53.8840.20081630.16923099326299
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)
13.80831.82731.58654.22511.40742.60270.0685-0.23110.2259-0.1732-0.11920.29640.2928-0.42010.14650.1913-0.0131-0.01440.18020.00670.16535.165612.156420.3027
26.5148-2.85462.29833.44032.18235.7021-0.19110.2459-1.3019-0.57040.37421.00751.4481-0.98320.57021.1709-0.2958-0.05190.3568-0.1170.495427.1043-9.89138.0702
31.1550.9547-0.00523.09990.0682.1645-0.1742-0.07240.0236-0.01820.0329-0.34790.05260.10090.14050.15240.01260.01390.1615-0.01030.229746.750111.649524.7918
45.84025.79923.24876.52182.26115.5104-0.4210.11560.0592-1.36240.2398-0.47290.05320.0520.24970.2915-0.01950.0560.1701-0.01350.230939.482113.950111.8522
55.76424.44891.40853.33821.22671.903-0.1730.349-0.4365-0.21670.3464-0.6286-0.04140.356-0.13450.2801-0.03130.0770.2605-0.02770.292549.30649.268214.1847
62.74141.5695-0.37842.8055-0.48152.7819-0.12020.1853-0.4628-0.71660.0265-0.31980.20740.2250.00120.4117-0.03580.0670.2245-0.06090.270341.97512.679710.1561
72.13021.40140.72753.60661.80484.3617-0.34340.37680.0453-0.53930.28120.0110.331-0.02780.12910.3209-0.04880.06570.23450.00940.211537.99629.377711.035
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 163 through 193 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 194 through 216 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 217 through 259 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 260 through 270 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 271 through 299 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 300 through 348 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 349 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