[English] 日本語
Yorodumi
- PDB-2qku: The 5th PDZ Domain of InaD in 10mM DTT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qku
TitleThe 5th PDZ Domain of InaD in 10mM DTT
ComponentsInactivation-no-after-potential D protein
KeywordsPEPTIDE BINDING PROTEIN / PDZ DOMAIN / SCAFFOLDING PROTEIN / DISULFIDE BOND / Membrane / Sensory transduction / Vision
Function / homology
Function and homology information


myosin III binding / detection of light stimulus involved in sensory perception / inaD signaling complex / negative regulation of opsin-mediated signaling pathway / rhabdomere / cellular response to light stimulus / myosin binding / photoreceptor activity / phototransduction / visual perception ...myosin III binding / detection of light stimulus involved in sensory perception / inaD signaling complex / negative regulation of opsin-mediated signaling pathway / rhabdomere / cellular response to light stimulus / myosin binding / photoreceptor activity / phototransduction / visual perception / sensory perception of sound / protein localization / signaling receptor complex adaptor activity / calmodulin binding
Similarity search - Function
PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Inactivation-no-after-potential D protein
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsRanganathan, R. / Socolich, M. / Wall, M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Dynamic Scaffolding in a G Protein-Coupled Signaling System.
Authors: Mishra, P. / Socolich, M. / Wall, M.A. / Graves, J. / Wang, Z. / Ranganathan, R.
History
DepositionJul 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Inactivation-no-after-potential D protein
B: Inactivation-no-after-potential D protein
C: Inactivation-no-after-potential D protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5995
Polymers29,4153
Non-polymers1842
Water4,792266
1
A: Inactivation-no-after-potential D protein


Theoretical massNumber of molelcules
Total (without water)9,8051
Polymers9,8051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Inactivation-no-after-potential D protein
C: Inactivation-no-after-potential D protein
hetero molecules

B: Inactivation-no-after-potential D protein
C: Inactivation-no-after-potential D protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5888
Polymers39,2204
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+1,y,-z1
MethodPISA
Unit cell
Length a, b, c (Å)67.700, 67.700, 162.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
DetailsThe biological assembly is unknown.

-
Components

#1: Protein Inactivation-no-after-potential D protein


Mass: 9804.991 Da / Num. of mol.: 3 / Fragment: 5th PDZ Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: inaD / Plasmid: pGEX-5X-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q24008
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 3.16 Å3/Da / Density % sol: 61.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.3M Na Citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL1-510.97965
SYNCHROTRONSSRL BL1-520.980035
SYNCHROTRONSSRL BL1-530.925256
SYNCHROTRONSSRL BL1-541.06883
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDMar 18, 2000
2
3
4
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double-crystal monochromatorMADMx-ray1
2Mx-ray1
3Mx-ray1
4Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979651
20.9800351
30.9252561
41.068831
ReflectionResolution: 2.2→40 Å / Num. obs: 35921 / % possible obs: 97.9 % / Biso Wilson estimate: 14.5 Å2 / Rsym value: 0.116 / Net I/σ(I): 10.4
Reflection shellResolution: 2.2→2.41 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.553 / % possible all: 96

-
Processing

Software
NameVersionClassificationNB
CNS1refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→29.77 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 83924.781 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1700 5 %RANDOM
Rwork0.206 ---
obs0.206 33753 92.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.789 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 24 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å20 Å2
2--1.5 Å20 Å2
3----3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1973 0 12 266 2251
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
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_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it22
X-RAY DIFFRACTIONc_scbond_it2.432
X-RAY DIFFRACTIONc_scangle_it3.462.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.305 266 5.2 %
Rwork0.276 4898 -
obs--84.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3glycerol.paramglycerol.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