[English] 日本語
Yorodumi
- PDB-1jh7: Semi-reduced Inhibitor-bound Cyclic Nucleotide Phosphodiesterase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jh7
TitleSemi-reduced Inhibitor-bound Cyclic Nucleotide Phosphodiesterase from Arabidopsis thaliana
Componentscyclic phosphodiesterase
KeywordsHYDROLASE / ADP-ribose 1'' / 2''-cyclic phosphate / RNA processing / 2' / 3'-cyclic nucleotide phosphodiesterase / 3'-cyclic uridine vanadate
Function / homology
Function and homology information


cyclic-nucleotide phosphodiesterase activity / 2',3'-cyclic-nucleotide 3'-phosphodiesterase / tRNA splicing, via endonucleolytic cleavage and ligation / cytosol / cytoplasm
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
URIDINE-2',3'-VANADATE / Cyclic phosphodiesterase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHofmann, A. / Grella, M. / Botos, I. / Filipowicz, W. / Wlodawer, A.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structures of the semireduced and inhibitor-bound forms of cyclic nucleotide phosphodiesterase from Arabidopsis thaliana.
Authors: Hofmann, A. / Grella, M. / Botos, I. / Filipowicz, W. / Wlodawer, A.
History
DepositionJun 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5817
Polymers21,5101
Non-polymers1,0716
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: cyclic phosphodiesterase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)135,48542
Polymers129,0626
Non-polymers6,42336
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation16_545y+1/3,x-1/3,-z+2/31
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
Buried area24670 Å2
ΔGint-385 kcal/mol
Surface area46230 Å2
MethodPISA
3
A: cyclic phosphodiesterase
hetero molecules

A: cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,16214
Polymers43,0212
Non-polymers2,14112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
MethodPQS
Unit cell
Length a, b, c (Å)101.140, 101.140, 90.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-213-

SO4

21A-214-

SO4

31A-214-

SO4

41A-215-

SO4

51A-215-

SO4

61A-377-

HOH

71A-392-

HOH

81A-393-

HOH

91A-394-

HOH

-
Components

#1: Protein cyclic phosphodiesterase


Mass: 21510.268 Da / Num. of mol.: 1
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, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-UVC / URIDINE-2',3'-VANADATE


Mass: 343.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12N2O9V
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5
Details: (NH4)2SO4, NaOAc, DTT, 2',3'-cyclic uridine vanadate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.2-2.0 Mammonium sulfate1reservoir
20.1 M1reservoirpH5.0NaOAc
312.5 mMDTT1drop
4100 mM1dropNaCl
520 mMTris-HCl1droppH8.0
610 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.07 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 11, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 7212 / Num. obs: 7212 / % possible obs: 90.3 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 38.4 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 15
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3 % / Rmerge(I) obs: 0.466 / % possible all: 95.4
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 5960 / Num. measured all: 87738
Reflection shell
*PLUS
% possible obs: 95.4 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: semi-reduced CPDase (A. thaliana) [delta 90-115]

Resolution: 2.4→25.29 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 185038.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.399 650 10.9 %RANDOM
Rwork0.214 ---
obs-5960 84.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 236.9 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso mean: 59.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å26.95 Å20 Å2
2--0.85 Å20 Å2
3----1.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.85 Å0.64 Å
Refinement stepCycle: LAST / Resolution: 2.4→25.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1458 0 62 94 1614
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.653
X-RAY DIFFRACTIONc_mcangle_it4.243.5
X-RAY DIFFRACTIONc_scbond_it4.093.5
X-RAY DIFFRACTIONc_scangle_it6.014
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.477 97 10.5 %
Rwork0.431 829 -
obs--79.8 %
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
X-RAY DIFFRACTION5UVD_NEU2.PARAMUVD_NEU2.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 10.9 % / Rfactor obs: 0.213 / Rfactor Rfree: 0.398
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 59.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.02
X-RAY DIFFRACTIONc_mcbond_it2.653
X-RAY DIFFRACTIONc_scbond_it4.093.5
X-RAY DIFFRACTIONc_mcangle_it4.243.5
X-RAY DIFFRACTIONc_scangle_it6.014
LS refinement shell
*PLUS
Rfactor Rfree: 0.477 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.431

+
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