[English] 日本語
Yorodumi
- PDB-4ojv: Crystal structure of unliganded yeast PDE1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ojv
TitleCrystal structure of unliganded yeast PDE1
Components3',5'-cyclic-nucleotide phosphodiesterase 1
KeywordsHYDROLASE / phosphodiesterase / cGMP and cAMP / yeast PDE / dual specificity
Function / homology
Function and homology information


negative regulation of glucose mediated signaling pathway / 3',5'-cyclic-nucleotide phosphodiesterase / cAMP catabolic process / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity
Similarity search - Function
Cyclic-AMP phosphodiesterase, class-II / Cyclic-AMP phosphodiesterase class-II, conserved site / cAMP phosphodiesterases class-II / cAMP phosphodiesterases class-II signature. / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
3',5'-cyclic-nucleotide phosphodiesterase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.31 Å
AuthorsTian, Y. / Cui, W. / Huang, M. / Robinson, H. / Wan, Y. / Wang, Y. / Ke, H.
CitationJournal: Biochemistry / Year: 2014
Title: Dual specificity and novel structural folding of yeast phosphodiesterase-1 for hydrolysis of second messengers cyclic adenosine and guanosine 3',5'-monophosphate.
Authors: Tian, Y. / Cui, W. / Huang, M. / Robinson, H. / Wan, Y. / Wang, Y. / Ke, H.
History
DepositionJan 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: 3',5'-cyclic-nucleotide phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4155
Polymers42,0701
Non-polymers3454
Water4,468248
1
A: 3',5'-cyclic-nucleotide phosphodiesterase 1
hetero molecules

A: 3',5'-cyclic-nucleotide phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,83010
Polymers84,1402
Non-polymers6908
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area7260 Å2
ΔGint-269 kcal/mol
Surface area28170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.478, 85.151, 130.565
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein 3',5'-cyclic-nucleotide phosphodiesterase 1 / PDEase 1 / 3':5'-CNP / Low-affinity cAMP phosphodiesterase


Mass: 42070.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: PDE1, YGL248W, NRB369 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P22434, 3',5'-cyclic-nucleotide phosphodiesterase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: The native crystal of yPDE1 (6 mg/ml) was grown by hanging drop against a buffer of 20 mM HEPES pH 7.5, 5% PEG3350, 40 mM Li sulfate, and 12% MPD at room temperature, or a similar buffer but ...Details: The native crystal of yPDE1 (6 mg/ml) was grown by hanging drop against a buffer of 20 mM HEPES pH 7.5, 5% PEG3350, 40 mM Li sulfate, and 12% MPD at room temperature, or a similar buffer but 15% glycerol and 20% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.05 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2013
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.31→30 Å / Num. all: 96740 / Num. obs: 96740 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 12.6

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.31→27.81 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.169 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1843 4844 5 %RANDOM
Rwork0.17212 ---
obs0.17274 96740 98.4 %-
all-96740 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.009 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.31→27.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2913 0 15 248 3176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022999
X-RAY DIFFRACTIONr_angle_refined_deg1.2051.9784053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5725361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15224.444135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.47615537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.061515
X-RAY DIFFRACTIONr_chiral_restr0.080.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212230
X-RAY DIFFRACTIONr_rigid_bond_restr2.29532999
X-RAY DIFFRACTIONr_sphericity_free14.791557
X-RAY DIFFRACTIONr_sphericity_bonded5.72553120
LS refinement shellResolution: 1.31→1.348 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 321 -
Rwork0.263 6419 -
obs--98.84 %

+
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