[English] 日本語
Yorodumi
- PDB-3rty: Structure of an Enclosed Dimer Formed by The Drosophila Period Protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rty
TitleStructure of an Enclosed Dimer Formed by The Drosophila Period Protein
ComponentsPeriod circadian protein
KeywordsCIRCADIAN CLOCK PROTEIN / PAS domain / signalling / Timeless
Function / homology
Function and homology information


Nuclear import of PER and TIM / Dephosphorylation of TIM / eclosion rhythm / Transcription repression by PER and activation by PDP1 / Dephosphorylation of PER / Phosphorylation of PER and TIM / copulation / Degradation of PER / Degradation of TIM / male courtship behavior, veined wing generated song production ...Nuclear import of PER and TIM / Dephosphorylation of TIM / eclosion rhythm / Transcription repression by PER and activation by PDP1 / Dephosphorylation of PER / Phosphorylation of PER and TIM / copulation / Degradation of PER / Degradation of TIM / male courtship behavior, veined wing generated song production / circadian temperature homeostasis / circadian sleep/wake cycle / courtship behavior / rhythmic behavior / regulation of locomotor rhythm / regulation of circadian sleep/wake cycle, sleep / entrainment of circadian clock / circadian behavior / mating behavior / response to temperature stimulus / entrainment of circadian clock by photoperiod / locomotor rhythm / response to light stimulus / long-term memory / behavioral response to cocaine / transcription corepressor binding / determination of adult lifespan / transcription coregulator activity / circadian regulation of gene expression / circadian rhythm / regulation of circadian rhythm / transcription corepressor activity / cell body / response to oxidative stress / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / PAS domain / PAS domain / Beta-Lactamase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily ...: / PAS domain / PAS domain / Beta-Lactamase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Period circadian protein
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsKing, H.A. / Hoelz, A. / Crane, B.R. / Young, M.W.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structure of an enclosed dimer formed by the Drosophila period protein.
Authors: King, H.A. / Hoelz, A. / Crane, B.R. / Young, M.W.
History
DepositionMay 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Period circadian protein
B: Period circadian protein
C: Period circadian protein
D: Period circadian protein
E: Period circadian protein
F: Period circadian protein
G: Period circadian protein
H: Period circadian protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,81436
Polymers305,4958
Non-polymers4,31928
Water4,197233
1
A: Period circadian protein
B: Period circadian protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,60810
Polymers76,3742
Non-polymers1,2348
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-76 kcal/mol
Surface area30910 Å2
MethodPISA
2
C: Period circadian protein
D: Period circadian protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4549
Polymers76,3742
Non-polymers1,0807
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-73 kcal/mol
Surface area30780 Å2
MethodPISA
3
E: Period circadian protein
F: Period circadian protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2998
Polymers76,3742
Non-polymers9266
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-74 kcal/mol
Surface area30880 Å2
MethodPISA
4
G: Period circadian protein
H: Period circadian protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4549
Polymers76,3742
Non-polymers1,0807
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-75 kcal/mol
Surface area30760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.414, 94.697, 141.030
Angle α, β, γ (deg.)88.19, 89.63, 89.87
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Period circadian protein / Protein clock-6 / CLK-6


Mass: 38186.922 Da / Num. of mol.: 8 / Fragment: central fragment (UNP residues 236-574)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: per, CG2647 / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07663
#2: Chemical...
ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 200 mM lithium chloride, 20 % (w/v) PEG 3350, 100 mM Bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→30 Å / Num. obs: 62952 / % possible obs: 92.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 87.3 Å2 / Rsym value: 0.081 / Net I/σ(I): 14.2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→20.01 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 74354.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.289 6399 10.2 %RANDOM
Rwork0.239 ---
obs0.239 62959 92.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.1009 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 70.1 Å2
Baniso -1Baniso -2Baniso -3
1-5.58 Å22.55 Å21.42 Å2
2--3.28 Å2-1.29 Å2
3----8.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.85→20.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19391 0 224 233 19848
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.41
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.71.5
X-RAY DIFFRACTIONc_mcangle_it3.082
X-RAY DIFFRACTIONc_scbond_it6.272
X-RAY DIFFRACTIONc_scangle_it7.632.5
LS refinement shellResolution: 2.85→3.03 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.4 889 10.7 %
Rwork0.345 7443 -
obs--68.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6DTT.top

+
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