[English] 日本語
Yorodumi
- PDB-3n89: KH domains -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3n89
TitleKH domains
ComponentsDefective in germ line development protein 3, isoform a
KeywordsCELL CYCLE / KH domains / RNA binding / germline development
Function / homology
Function and homology information


germ-line sex determination / polynucleotide adenylyltransferase activator activity / masculinization of hermaphroditic germ-line / vulval development / nematode larval development / cytosolic mRNA polyadenylation / germ-line stem cell division / RNA-directed RNA polymerase complex / positive regulation of meiosis I / nuclear division ...germ-line sex determination / polynucleotide adenylyltransferase activator activity / masculinization of hermaphroditic germ-line / vulval development / nematode larval development / cytosolic mRNA polyadenylation / germ-line stem cell division / RNA-directed RNA polymerase complex / positive regulation of meiosis I / nuclear division / positive regulation of meiotic nuclear division / embryo development ending in birth or egg hatching / positive regulation of multicellular organism growth / P granule / RNA polymerase complex / mitotic cytokinesis / positive regulation of mitotic nuclear division / meiotic cell cycle / mRNA processing / regulation of translation / spermatogenesis / protein domain specific binding / positive regulation of gene expression / perinuclear region of cytoplasm / RNA binding / cytoplasm
Similarity search - Function
TATA-Binding Protein - #270 / GLD-3, KH5 domain / : / : / : / : / GLD-3 4th KH domain (aka KH5) / GLD-3 2nd KH domain (aka KH3) / GLD-3 3rd KH domain (aka KH4) / GLD-3 1st KH domain (aka KH2) ...TATA-Binding Protein - #270 / GLD-3, KH5 domain / : / : / : / : / GLD-3 4th KH domain (aka KH5) / GLD-3 2nd KH domain (aka KH3) / GLD-3 3rd KH domain (aka KH4) / GLD-3 1st KH domain (aka KH2) / TATA-Binding Protein - #210 / TATA-Binding Protein / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Defective in germ line development protein 3
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.789 Å
AuthorsNakel, K. / Hartung, S.A. / Bonneau, F. / Eckmann, C.R. / Conti, E.
CitationJournal: Rna / Year: 2010
Title: Four KH domains of the C. elegans Bicaudal-C ortholog GLD-3 form a globular structural platform.
Authors: Nakel, K. / Hartung, S.A. / Bonneau, F. / Eckmann, C.R. / Conti, E.
History
DepositionMay 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Defective in germ line development protein 3, isoform a
B: Defective in germ line development protein 3, isoform a


Theoretical massNumber of molelcules
Total (without water)85,7542
Polymers85,7542
Non-polymers00
Water77543
1
A: Defective in germ line development protein 3, isoform a


Theoretical massNumber of molelcules
Total (without water)42,8771
Polymers42,8771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Defective in germ line development protein 3, isoform a


Theoretical massNumber of molelcules
Total (without water)42,8771
Polymers42,8771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Defective in germ line development protein 3, isoform a

B: Defective in germ line development protein 3, isoform a


Theoretical massNumber of molelcules
Total (without water)85,7542
Polymers85,7542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area1830 Å2
ΔGint-12 kcal/mol
Surface area31810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.504, 102.241, 83.608
Angle α, β, γ (deg.)90.00, 119.32, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Defective in germ line development protein 3, isoform a


Mass: 42876.961 Da / Num. of mol.: 2 / Fragment: UNP residues 88-460
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: gld-3, T07F8.3 / Plasmid: pETM30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold pLyS / References: UniProt: Q95ZK7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 3.48 Å3/Da / Density % sol: 64.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Ammoniumsulfate, Hepes, Glycerol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06SA10.979
SYNCHROTRONSLS X06SA21
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDMar 26, 2009
MARMOSAIC 225 mm CCD2CCDFeb 25, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LN2 cooled fixed-exit Si(111) monochromatorMADMx-ray1
2LN2 cooled fixed-exit Si(111) monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
211
ReflectionResolution: 2.79→48.1 Å / Num. obs: 28664 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rsym value: 0.134 / Net I/σ(I): 8.61
Reflection shellResolution: 2.79→3.07 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 7600 / Rsym value: 0.593

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.789→48.113 Å / Occupancy max: 1 / Occupancy min: 0 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1489 5.1 %RANDOM
Rwork0.259 ---
all-28616 --
obs-28617 97.8 %-
Solvent computationBsol: 50.023 Å2
Displacement parametersBiso max: 59.8 Å2 / Biso mean: 31.207 Å2 / Biso min: 10.19 Å2
Baniso -1Baniso -2Baniso -3
1--1.754 Å20 Å23.445 Å2
2---0.579 Å20 Å2
3---2.333 Å2
Refinement stepCycle: LAST / Resolution: 2.789→48.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5274 0 0 43 5317
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.214
X-RAY DIFFRACTIONc_mcbond_it1.1921.5
X-RAY DIFFRACTIONc_scbond_it1.7122
X-RAY DIFFRACTIONc_mcangle_it1.952
X-RAY DIFFRACTIONc_scangle_it2.3762.5
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.paramCNS_TOPPAR:ion.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