[English] 日本語
Yorodumi
- PDB-1fsi: CRYSTAL STRUCTURE OF CYCLIC NUCLEOTIDE PHOSPHODIESTERASE OF APPR>... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fsi
TitleCRYSTAL STRUCTURE OF CYCLIC NUCLEOTIDE PHOSPHODIESTERASE OF APPR>P FROM ARABIDOPSIS THALIANA
ComponentsCYCLIC PHOSPHODIESTERASE
KeywordsHYDROLASE / ADP-ribose 1'' / 2''-cyclic phosphate / Appr>p / 2' / 3'-cyclic nucleotide phosphodiesterase
Function / homology
Function and homology information


cyclic-nucleotide phosphodiesterase activity / 2',3'-cyclic-nucleotide 3'-phosphodiesterase / tRNA splicing, via endonucleolytic cleavage and ligation / cytoplasm / cytosol
Similarity search - Function
2',3'-cyclic-nucleotide 3'-phosphodiesterase / Cyclic phosphodiesterase-like protein / Cyclic Phosphodiesterase; Chain: A, / Cyclic phosphodiesterase / Cyclic phosphodiesterase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Cyclic phosphodiesterase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR/MAD / Resolution: 2.5 Å
AuthorsHofmann, A. / Zdanov, A. / Genschik, P. / Filipowicz, W. / Ruvinov, S. / Wlodawer, A.
Citation
Journal: EMBO J. / Year: 2000
Title: Structure and mechanism of activity of the cyclic phosphodiesterase of Appr>p, a product of the tRNA splicing reaction.
Authors: Hofmann, A. / Zdanov, A. / Genschik, P. / Ruvinov, S. / Filipowicz, W. / Wlodawer, A.
#1: Journal: J.Biol.Chem. / Year: 1997
Title: Cloning and Characterization of the Arabidopsis cyclic phosphodiesterase which hydrolyzes ADP-ribose 1'',2''-cyclic phosphate and nucleoside 2',3'-cyclic phosphates
Authors: Genschik, P. / Hall, J. / Filipowicz, W.
History
DepositionSep 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CYCLIC PHOSPHODIESTERASE
B: CYCLIC PHOSPHODIESTERASE
C: CYCLIC PHOSPHODIESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,39512
Polymers64,5313
Non-polymers8659
Water4,125229
1
A: CYCLIC PHOSPHODIESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7984
Polymers21,5101
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CYCLIC PHOSPHODIESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7984
Polymers21,5101
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CYCLIC PHOSPHODIESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7984
Polymers21,5101
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
A: CYCLIC PHOSPHODIESTERASE
B: CYCLIC PHOSPHODIESTERASE
C: CYCLIC PHOSPHODIESTERASE
hetero molecules

A: CYCLIC PHOSPHODIESTERASE
B: CYCLIC PHOSPHODIESTERASE
C: CYCLIC PHOSPHODIESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,79124
Polymers129,0626
Non-polymers1,72918
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area17690 Å2
ΔGint-329 kcal/mol
Surface area43740 Å2
MethodPISA
5
C: CYCLIC PHOSPHODIESTERASE
hetero molecules

C: CYCLIC PHOSPHODIESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5978
Polymers43,0212
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area3110 Å2
ΔGint-125 kcal/mol
Surface area17350 Å2
MethodPISA
6
B: CYCLIC PHOSPHODIESTERASE
hetero molecules

A: CYCLIC PHOSPHODIESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5978
Polymers43,0212
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area2590 Å2
ΔGint-92 kcal/mol
Surface area17890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.916, 125.916, 209.897
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2
Detailsmost likely monomeric

-
Components

#1: Protein CYCLIC PHOSPHODIESTERASE


Mass: 21510.268 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: PET11D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O04147
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.68 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.9 M (NH4)2SO4, 0.1 M NaAc, 10% EtOH, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
2100 mM1dropNaCl
320 mMTris-HCl1drop
41.0 Mammonium sulfate1reservoir
50.1 M1reservoirNaOAc

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONNSLS X9B11.0094
SYNCHROTRONNSLS X9B21.006
SYNCHROTRONNSLS X9B30.9537
SYNCHROTRONNSLS X9B4
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDFeb 4, 2000
ADSC QUANTUM 42CCDFeb 4, 2000
ADSC QUANTUM 43CCDFeb 4, 2000
ADSC QUANTUM 44CCDFeb 4, 2000
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
4SINGLE WAVELENGTHMx-ray4
Radiation wavelength
IDWavelength (Å)Relative weight
11.00941
21.0061
30.95371
41
ReflectionResolution: 2.5→20 Å / Num. obs: 34305 / % possible obs: 98.8 % / Redundancy: 18 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.081
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6 % / Rmerge(I) obs: 0.144 / % possible all: 97.8
Reflection
*PLUS
Num. measured all: 1085650
Reflection shell
*PLUS
% possible obs: 97.8 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
CNS1refinement
RefinementMethod to determine structure: SIR/MAD / Resolution: 2.5→19.91 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 58916.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2782 9.8 %RANDOM
Rwork0.196 ---
obs0.196 28263 81.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.86 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso mean: 47 Å2
Baniso -1Baniso -2Baniso -3
1-13.06 Å213.28 Å20 Å2
2--13.06 Å20 Å2
3----26.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4139 0 45 229 4413
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d1.2
X-RAY DIFFRACTIONc_mcbond_it3.113.5
X-RAY DIFFRACTIONc_mcangle_it4.614
X-RAY DIFFRACTIONc_scbond_it5.14
X-RAY DIFFRACTIONc_scangle_it6.664.5
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)
11CONSTRX-RAY DIFFRACTION0.2459
22X-RAY DIFFRACTION0.1738
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.362 327 9.6 %
Rwork0.288 3092 -
obs--60.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 9.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 47 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.2
X-RAY DIFFRACTIONc_mcbond_it3.5
X-RAY DIFFRACTIONc_scbond_it4
X-RAY DIFFRACTIONc_mcangle_it4
X-RAY DIFFRACTIONc_scangle_it4.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.362 / % reflection Rfree: 9.6 % / Rfactor Rwork: 0.288 / Rfactor obs: 0.288

+
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://pdbjlvh1.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