[English] 日本語
Yorodumi
- PDB-4it6: Crystal structure of amino acid residues 1-120 of CG17282 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4it6
TitleCrystal structure of amino acid residues 1-120 of CG17282
ComponentsCG17282
KeywordsUNKNOWN FUNCTION / FK506-binding protein / Ubiquitous
Function / homology
Function and homology information


regulation of post-translational protein modification / regulation of establishment of planar polarity / kinase activator activity / regulation of protein catabolic process / regulation of intracellular protein transport / locomotor rhythm / cytosol
Similarity search - Function
Elongation Factor Tu (Ef-tu); domain 3 - #320 / BDBT FKBP like, N-terminal / : / BDBT FKBP like N-terminal / Bride of doubletime-like, TPR domain / Elongation Factor Tu (Ef-tu); domain 3 / Tetratricopeptide-like helical domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
FORMIC ACID / DI(HYDROXYETHYL)ETHER / Protein Bride of doubletime
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsBouyain, S. / Agyekum, B. / Hall, D.R.
CitationJournal: Neuron / Year: 2013
Title: Noncanonical FK506-Binding Protein BDBT Binds DBT to Enhance Its Circadian Function and Forms Foci at Night.
Authors: Fan, J.Y. / Agyekum, B. / Venkatesan, A. / Hall, D.R. / Keightley, A. / Bjes, E.S. / Bouyain, S. / Price, J.L.
History
DepositionJan 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CG17282
B: CG17282
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,40511
Polymers27,8712
Non-polymers5349
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-17 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.503, 46.461, 69.146
Angle α, β, γ (deg.)90.000, 105.640, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein CG17282 / RE50353p


Mass: 13935.392 Da / Num. of mol.: 2 / Fragment: UNP Residues 1-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG17282, Dmel_CG17282 / Plasmid: pT7HMP / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9VDE4
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 49.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 4M sodium formate pH 6.9, 0.1 M Na-cacodylate pH 6.5 and 1% (w/v) polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97243, 0.97934
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 7, 2011
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.972431
20.979341
ReflectionRedundancy: 6.4 % / Av σ(I) over netI: 13.98 / Number: 130707 / Rmerge(I) obs: 0.117 / Χ2: 0.97 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 20305 / % possible obs: 95.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.095099.410.0820.9727.1
3.254.0999.310.1011.057
2.843.2599.210.1230.937.2
2.582.8499.410.1670.9547.4
2.392.5899.310.2071.0747.2
2.252.3999.210.2550.9537
2.142.2598.910.290.966.4
2.052.1497.110.3330.9115.6
1.972.0590.910.3980.9344.7
1.91.9773.510.4470.7633.8
ReflectionResolution: 1.9→50 Å / Num. obs: 20495 / % possible obs: 96.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.114 / Χ2: 0.997 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.973.30.49915670.999174.5
1.97-2.054.40.4219620.906192.6
2.05-2.145.40.35420730.968197.7
2.14-2.2560.29520891.047199
2.25-2.396.70.26920911.033199.4
2.39-2.587.20.22121240.993199.6
2.58-2.847.50.17621140.994199.6
2.84-3.257.40.1221300.977199.8
3.25-4.097.30.09721521.008199.8
4.09-507.20.07621931.009199.6

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→30.412 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.775 / SU ML: 0.66 / σ(F): 2 / Phase error: 29.38 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2796 1948 9.74 %RANDOM
Rwork0.2611 ---
obs0.2629 20004 93.63 %-
all-21952 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.733 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso max: 64.54 Å2 / Biso mean: 30.7034 Å2 / Biso min: 18.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.1383 Å20 Å23.4595 Å2
2--3.8462 Å2-0 Å2
3----6.9845 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.412 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 0 35 131 1962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081852
X-RAY DIFFRACTIONf_angle_d1.0962481
X-RAY DIFFRACTIONf_chiral_restr0.077288
X-RAY DIFFRACTIONf_plane_restr0.004304
X-RAY DIFFRACTIONf_dihedral_angle_d16.157688
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.94530.3223860.282678587158
1.9453-1.99790.30651180.28421111122981
1.9979-2.05670.29711370.28411242137991
2.0567-2.1230.2941370.26931276141394
2.123-2.19890.28211420.26391329147197
2.1989-2.28690.32241420.25781329147198
2.2869-2.39090.27731470.26711342148997
2.3909-2.51690.29641410.2721335147698
2.5169-2.67450.2961500.28441366151699
2.6745-2.88090.35581460.2871378152499
2.8809-3.17050.27591480.27651359150799
3.1705-3.62870.28341480.235313781526100
3.6287-4.56930.21451530.209214061559100
4.5693-30.4120.28651530.29241420157399

+
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