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- PDB-5qsw: PanDDA analysis group deposition -- Crystal Structure of human ST... -

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Basic information

Entry
Database: PDB / ID: 5qsw
TitlePanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2856434884
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 / Resolution of Sister Chromatid Cohesion / Meiotic synapsis / nuclear matrix / Separation of Sister Chromatids / chromosome / Estrogen-dependent gene expression / nuclear body / cell division / chromatin binding / chromatin / nucleoplasm / nucleus / cytosol
Similarity search - Function
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
1-[4-(3-phenylpropyl)piperazin-1-yl]ethan-1-one / Cohesin subunit SA-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 3.03 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)159,5048
Polymers158,5184
Non-polymers9854
Water2,828157
1
C: Cohesin subunit SA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8762
Polymers39,6301
Non-polymers2461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cohesin subunit SA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8762
Polymers39,6301
Non-polymers2461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Cohesin subunit SA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8762
Polymers39,6301
Non-polymers2461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cohesin subunit SA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8762
Polymers39,6301
Non-polymers2461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.489, 72.409, 118.515
Angle α, β, γ (deg.)94.890, 98.600, 115.590
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 39629.531 Da / Num. of mol.: 4
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-O3J / 1-[4-(3-phenylpropyl)piperazin-1-yl]ethan-1-one


Mass: 246.348 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.13 % / 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

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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: Sep 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 3.03→115.5 Å / Num. obs: 37042 / % possible obs: 98.3 % / Redundancy: 1.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.072 / Rrim(I) all: 0.101 / Net I/σ(I): 6.4 / Num. measured all: 65596 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.03-3.111.80.635498527470.610.6350.8981.198.1
13.55-115.51.90.0288174200.9810.0280.042199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
Aimless0.7.2data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6qb5

6qb5


Resolution: 3.03→115.52 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.9 / SU B: 23.017 / SU ML: 0.386 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.451 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2672 1844 5 %RANDOM
Rwork0.1873 ---
obs0.1914 35191 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 251.18 Å2 / Biso mean: 90.959 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-2.94 Å22.17 Å23.56 Å2
2---0.42 Å21.09 Å2
3----5.93 Å2
Refinement stepCycle: final / Resolution: 3.03→115.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10037 0 72 157 10266
Biso mean--54.4 82.18 -
Num. residues----1221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01310442
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179903
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.64614042
X-RAY DIFFRACTIONr_angle_other_deg1.2761.58922901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.11251236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.01722.082610
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.116152004
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3961585
X-RAY DIFFRACTIONr_chiral_restr0.070.21350
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211661
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022290
X-RAY DIFFRACTIONr_mcbond_it7.59.4394962
X-RAY DIFFRACTIONr_mcbond_other7.4999.4394963
X-RAY DIFFRACTIONr_mcangle_it11.11414.1336204
LS refinement shellResolution: 3.03→3.109 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 137 -
Rwork0.332 2540 -
all-2677 -
obs--95.92 %

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