[English] 日本語
Yorodumi
- PDB-4eq6: The crystal structure of Psy3-Csm2 complex from budding yeast -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4eq6
TitleThe crystal structure of Psy3-Csm2 complex from budding yeast
Components
  • Chromosome segregation in meiosis protein 2
  • Platinum sensitivity protein 3
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


Shu complex / positive regulation of single-strand break repair via homologous recombination / error-free postreplication DNA repair / meiotic chromosome segregation / maintenance of rDNA / DNA recombinase assembly / recombinational repair / error-free translesion synthesis / site of double-strand break / nucleus ...Shu complex / positive regulation of single-strand break repair via homologous recombination / error-free postreplication DNA repair / meiotic chromosome segregation / maintenance of rDNA / DNA recombinase assembly / recombinational repair / error-free translesion synthesis / site of double-strand break / nucleus / cytoplasm / cytosol
Similarity search - Function
Shu complex, component Psy3 / Chromosome segregation in meiosis protein 2 / Shu complex component Csm2, DNA-binding / Shu complex component Psy3, DNA-binding description / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chromosome segregation in meiosis protein 2 / Platinum sensitivity protein 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsShe, Z. / Gao, Z.Q. / Dong, Y.H.
CitationJournal: FEBS Lett. / Year: 2012
Title: Structural and SAXS analysis of the budding yeast SHU-complex proteins
Authors: She, Z. / Gao, Z.Q. / Liu, Y. / Wang, W.J. / Liu, G.F. / Shtykova, E.V. / Xu, J.H. / Dong, Y.H.
History
DepositionApr 18, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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: Chromosome segregation in meiosis protein 2
B: Platinum sensitivity protein 3


Theoretical massNumber of molelcules
Total (without water)54,9592
Polymers54,9592
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-6 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.333, 51.162, 77.049
Angle α, β, γ (deg.)90.00, 103.02, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-303-

HOH

-
Components

#1: Protein Chromosome segregation in meiosis protein 2


Mass: 25114.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CSM2, YIL132C / Plasmid: pCDFDuet / Production host: Escherichia coli (E. coli) / References: UniProt: P40465
#2: Protein Platinum sensitivity protein 3


Mass: 29844.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: PSY3, YLR376C, L8039.17 / Plasmid: pCDFDuet / Production host: Escherichia coli (E. coli) / References: UniProt: Q12318
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.36 Å3/Da / Density % sol: 47.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100mM Tris-HCl, pH 8.0, 10% ethanol, 10% 2-methyl-2,4-pentadiol (MPD), VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2011
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. all: 46537 / Num. obs: 43595 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 38.9
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2353 / % possible all: 91.9

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.855 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 24.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2169 5.05 %RANDOM
Rwork0.2014 ---
all0.2028 44184 --
obs0.2014 42983 89.73 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.963 Å2 / ksol: 0.355 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.6046 Å2-0 Å2-3.5129 Å2
2--9.9376 Å20 Å2
3----7.3329 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3170 0 0 162 3332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073233
X-RAY DIFFRACTIONf_angle_d1.1374380
X-RAY DIFFRACTIONf_dihedral_angle_d14.1281184
X-RAY DIFFRACTIONf_chiral_restr0.082518
X-RAY DIFFRACTIONf_plane_restr0.005547
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.84190.30981530.246730213174100
1.8419-1.88790.30131500.27293023317399
1.8879-1.9390.5525890.46451471156050
1.939-1.9960.29881740.25132989316399
1.996-2.06040.26361570.19930013158100
2.0604-2.1340.23971680.196130343202100
2.134-2.21940.26841320.20422977310999
2.2194-2.32040.2551800.22331499157949
2.3204-2.44270.22611710.20229993170100
2.4427-2.59570.22131390.206530253164100
2.5957-2.79590.24281700.203830303200100
2.7959-3.07710.23031790.212730083187100
3.0771-3.52170.24741530.20343036318999
3.5217-4.43470.17641070.16611830193760
4.4347-29.85920.18711470.18262871301891
Refinement TLS params.Method: refined / Origin x: -16.7614 Å / Origin y: 1.8044 Å / Origin z: -8.4787 Å
111213212223313233
T0.0212 Å2-0.0026 Å20.0112 Å2--0.0079 Å2-0.0258 Å2--0.1083 Å2
L1.4956 °2-0.1556 °20.5839 °2-0.8969 °2-0.4193 °2--3.1858 °2
S0.0209 Å °-0.1549 Å °-0.018 Å °-0.0297 Å °-0.0483 Å °0.1595 Å °0.0561 Å °-0.3202 Å °0.0122 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 213
2X-RAY DIFFRACTION1allB1 - 237
3X-RAY DIFFRACTION1allA301 - 388
4X-RAY DIFFRACTION1allB301 - 374

+
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