[English] 日本語
Yorodumi
- PDB-6l3q: Crystal structure of Chaetomium thermophilum Utp15 C terminal domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6l3q
TitleCrystal structure of Chaetomium thermophilum Utp15 C terminal domain
ComponentsWD_REPEATS_REGION domain-containing protein
KeywordsNUCLEAR PROTEIN / 90S preribosome
Function / homology
Function and homology information


rRNA processing / nucleolus
Similarity search - Function
U3 small nucleolar RNA-associated protein 15, C-terminal / UTP15 C terminal / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. ...U3 small nucleolar RNA-associated protein 15, C-terminal / UTP15 C terminal / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
U3 small nucleolar RNA-associated protein 15 C-terminal domain-containing protein
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.702 Å
AuthorsChen, R.C. / Ye, K.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China91540201 China
CitationJournal: To Be Published
Title: Crystal structure of Chaetomium thermophilum Utp15 C terminal domain
Authors: Chen, R.C. / Ye, K.Q.
History
DepositionOct 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: WD_REPEATS_REGION domain-containing protein
B: WD_REPEATS_REGION domain-containing protein


Theoretical massNumber of molelcules
Total (without water)31,3672
Polymers31,3672
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-17 kcal/mol
Surface area13470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.188, 106.188, 59.081
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein WD_REPEATS_REGION domain-containing protein


Mass: 15683.536 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / Gene: CTHT_0063870 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G0SEI5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.88 %
Crystal growTemperature: 293.15 K / Method: evaporation / pH: 6.5 / Details: 1.6M MgSO4, 0.1M Mes / PH range: 6.0-8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 20360 / % possible obs: 99.9 % / Redundancy: 21.3 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 35.93
Reflection shellResolution: 2.7→2.75 Å / Mean I/σ(I) obs: 17.95 / Num. unique obs: 512 / CC1/2: 0.998

-
Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.702→36.286 Å / FOM work R set: 0.8188 / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.06 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2407 2053 10.08 %
Rwork0.1986 18307 -
obs0.2028 20360 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.14 Å2 / Biso mean: 36.02 Å2 / Biso min: 14.14 Å2
Refinement stepCycle: final / Resolution: 2.702→36.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1999 0 0 20 2019
Biso mean---25.24 -
Num. residues----254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082035
X-RAY DIFFRACTIONf_angle_d1.0622763
X-RAY DIFFRACTIONf_chiral_restr0.071321
X-RAY DIFFRACTIONf_plane_restr0.005353
X-RAY DIFFRACTIONf_dihedral_angle_d14.741745
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7021-2.76490.36141360.25871207100
2.7649-2.8340.31460.25841234100
2.834-2.91060.28561340.23261215100
2.9106-2.99620.31941360.24391205100
2.9962-3.09290.28741340.23451219100
3.0929-3.20340.31411400.23091239100
3.2034-3.33160.30651420.21281236100
3.3316-3.48310.28441320.21891221100
3.4831-3.66650.30471340.19711233100
3.6665-3.8960.20911320.18361224100
3.896-4.19640.19221420.16911227100
4.1964-4.6180.1831360.17331226100
4.618-5.28440.22011420.18151223100
5.2844-6.65110.22131440.20651215100
6.6511-36.280.19071230.1726118396

+
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