[English] 日本語
Yorodumi
- PDB-5loi: Crystal structure of Myceliophthora thermophila Rad26 (residues 3... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5loi
TitleCrystal structure of Myceliophthora thermophila Rad26 (residues 373-841)
ComponentsRad26
KeywordsSIGNALING PROTEIN / Rad26 (ATRIP) / Rad3 (ATR) / DNA-damage response (DDR) / kinase signaling
Function / homologyRad26-like, helical repeats / Rad26-like, helical repeats / Uncharacterized protein
Function and homology information
Biological speciesMyceliophthora thermophila ATCC 42464 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.153 Å
AuthorsAndersen, K.R.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Insights into Rad3 kinase recruitment from the crystal structure of the DNA damage checkpoint protein Rad26.
Authors: Andersen, K.R.
History
DepositionAug 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2May 31, 2017Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Rad26


Theoretical massNumber of molelcules
Total (without water)51,6981
Polymers51,6981
Non-polymers00
Water0
1
A: Rad26

A: Rad26


Theoretical massNumber of molelcules
Total (without water)103,3972
Polymers103,3972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3860 Å2
ΔGint-25 kcal/mol
Surface area37470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.783, 210.783, 104.766
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

-
Components

#1: Protein Rad26


Mass: 51698.379 Da / Num. of mol.: 1 / Fragment: UNP residues 373-841
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myceliophthora thermophila ATCC 42464 (fungus)
Gene: MYCTH_2305697 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LOBSTR / References: UniProt: G2QDY6

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.63 Å3/Da / Density % sol: 78.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M BIS-TRIS pH 6.5 10% (w/v) PEG 10K 0.2M Potassium sodium tartrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.15→105.4 Å / Num. all: 540544 / Num. obs: 20640 / % possible obs: 99.4 % / Redundancy: 26.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.025 / Net I/σ(I): 23
Reflection shellResolution: 3.15→3.27 Å / Redundancy: 26.8 % / Rmerge(I) obs: 4.781 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1932 / CC1/2: 0.612 / Rpim(I) all: 0.937 / % possible all: 95.07

-
Processing

Software
NameVersionClassification
PHENIX(dev_2614: ???)refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 3.153→105.391 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2351 3764 9.73 %
Rwork0.2074 --
obs0.2101 20526 99.4 %
all-38691 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.153→105.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3013 0 0 0 3013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093081
X-RAY DIFFRACTIONf_angle_d1.014205
X-RAY DIFFRACTIONf_dihedral_angle_d6.4151872
X-RAY DIFFRACTIONf_chiral_restr0.06504
X-RAY DIFFRACTIONf_plane_restr0.007535
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.55580.17770.63120.82340.82030.5287-1.91220.6138-0.2741-1.95421.4221-0.66650.47730.0442-0.00042.50450.21260.09682.0408-0.04161.7606166.9086147.73387.5051
21.1378-1.6201-1.08654.83480.44374.40010.0297-0.1258-0.54320.3304-0.04030.06451.12920.06540.00111.46110.34190.08851.4007-0.03671.3347149.019155.112910.926
31.2591-1.3476-1.08893.97990.77314.93710.1645-0.0683-0.3677-0.0408-0.0762-0.39150.29880.6152-0.00131.19460.16230.09851.38080.19981.4314149.7931170.803712.8191
42.42580.25442.1452.37340.35834.08380.39080.79660.34120.0948-0.03550.0081-0.2718-0.04310.00191.08750.16260.16061.14820.18281.3476142.0975181.895813.936
52.81-0.53383.2797.9986-0.3024.07630.24750.36640.574-0.43630.0122-0.1489-0.69810.10730.00081.30510.0350.21531.39950.26811.3432142.0067194.77035.1388
61.65680.22960.0864.04280.1182.5724-0.49680.2218-0.0901-1.29120.2247-0.14520.33710.05780.00161.87930.05550.05131.2970.25991.4395140.3512203.5664-3.9614
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 374 through 408 )
2X-RAY DIFFRACTION2chain 'A' and (resid 409 through 496 )
3X-RAY DIFFRACTION3chain 'A' and (resid 497 through 587 )
4X-RAY DIFFRACTION4chain 'A' and (resid 588 through 658 )
5X-RAY DIFFRACTION5chain 'A' and (resid 659 through 790 )
6X-RAY DIFFRACTION6chain 'A' and (resid 791 through 832 )

+
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