[English] 日本語
Yorodumi
- PDB-5qsn: PanDDA analysis group deposition -- Crystal Structure of human ST... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5qsn
TitlePanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z1272480091
ComponentsCohesin subunit SA-1
KeywordsTRANSCRIPTION / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer
Function / homology
Function and homology information


Cohesin Loading onto Chromatin / Establishment of Sister Chromatid Cohesion / cohesin complex / mitotic cohesin complex / establishment of mitotic sister chromatid cohesion / sister chromatid cohesion / mitotic spindle pole / chromosome, centromeric region / mitotic spindle assembly / SUMOylation of DNA damage response and repair proteins ...Cohesin Loading onto Chromatin / Establishment of Sister Chromatid Cohesion / cohesin complex / mitotic cohesin complex / establishment of mitotic sister chromatid cohesion / sister chromatid cohesion / mitotic spindle pole / chromosome, centromeric region / mitotic spindle assembly / SUMOylation of DNA damage response and repair proteins / Meiotic synapsis / Resolution of Sister Chromatid Cohesion / nuclear matrix / Separation of Sister Chromatids / chromosome / Estrogen-dependent gene expression / nuclear body / cilium / cell division / chromatin binding / chromatin / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / Cohesin subunit SCC3/SA, HEAT-repeats domain / STAG / Stromalin conservative domain / Cohesin subunit Scc3/SA / STAG domain / Stromalin conservative domain / Stromalin conservative (SCD) domain profile. / Armadillo-type fold
Similarity search - Domain/homology
(2R)-2-(methoxymethyl)-4-(pyridin-2-yl)morpholine / Cohesin subunit SA-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.66 Å
AuthorsNewman, J.A. / Katis, V.L. / Gavard, A.E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
CitationJournal: To Be Published
Title: PanDDA analysis group deposition
Authors: Newman, J.A. / Katis, V.L. / Gavard, A.E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
History
DepositionMay 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cohesin subunit SA-1
B: Cohesin subunit SA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,7143
Polymers105,5062
Non-polymers2081
Water2,774154
1
A: Cohesin subunit SA-1


Theoretical massNumber of molelcules
Total (without water)52,7531
Polymers52,7531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cohesin subunit SA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9612
Polymers52,7531
Non-polymers2081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.984, 167.688, 47.106
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1111-

HOH

-
Components

#1: Protein Cohesin subunit SA-1 / SCC3 homolog 1 / Stromal antigen 1


Mass: 52752.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAG1, SA1, SCC3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WVM7
#2: Chemical ChemComp-O2J / (2R)-2-(methoxymethyl)-4-(pyridin-2-yl)morpholine


Mass: 208.257 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.6 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Bis Tris Propane pH 7.0, 0.2 M Sodium Malonate, 20 % PEG 3350, 10 % Ethylene Glycol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.66→113.82 Å / Num. obs: 36436 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.061 / Rrim(I) all: 0.154 / Net I/σ(I): 7 / Num. measured all: 229809 / Scaling rejects: 2
Reflection shellResolution: 2.66→2.73 Å / % possible obs: 100 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) all: 1.3 / Mean I/σ(I) obs: 1.3 / Num. measured obs: 15843 / Num. unique obs: 2602 / CC1/2: 0.365 / Rpim(I) all: 0.433 / Rrim(I) all: 0.1073 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
Aimless0.6.2data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6r7o

6r7o


Resolution: 2.66→113.82 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 21.796 / SU ML: 0.392 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.631 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2879 1832 5 %RANDOM
Rwork0.2175 ---
obs0.2211 34533 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 193.13 Å2 / Biso mean: 75.092 Å2 / Biso min: 39.85 Å2
Baniso -1Baniso -2Baniso -3
1--5.66 Å20 Å2-0 Å2
2--0.67 Å20 Å2
3---4.99 Å2
Refinement stepCycle: final / Resolution: 2.66→113.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6922 0 15 154 7091
Biso mean--94.18 65.18 -
Num. residues----860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0137059
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176626
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.639534
X-RAY DIFFRACTIONr_angle_other_deg1.2341.57415397
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9465850
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.67323.733367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.509151311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9941532
X-RAY DIFFRACTIONr_chiral_restr0.0670.2929
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027711
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021388
X-RAY DIFFRACTIONr_mcbond_it5.9217.9043430
X-RAY DIFFRACTIONr_mcbond_other5.9187.9033429
X-RAY DIFFRACTIONr_mcangle_it9.11411.8274270
LS refinement shellResolution: 2.657→2.726 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 125 -
Rwork0.405 2440 -
all-2565 -
obs--97.98 %

+
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