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

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Basic information

Entry
Database: PDB / ID: 5qsx
TitlePanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z2856434812
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 / 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
4-[(3,4-dihydroisoquinolin-2(1H)-yl)methyl]phenol / Cohesin subunit SA-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.34 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
DepositionJul 16, 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)159,2367
Polymers158,5184
Non-polymers7183
Water2,828157
1
C: Cohesin subunit SA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8692
Polymers39,6301
Non-polymers2391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cohesin subunit SA-1


Theoretical massNumber of molelcules
Total (without water)39,6301
Polymers39,6301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Cohesin subunit SA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8692
Polymers39,6301
Non-polymers2391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cohesin subunit SA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8692
Polymers39,6301
Non-polymers2391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.723, 72.398, 118.428
Angle α, β, γ (deg.)94.820, 98.370, 115.510
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-O3M / 4-[(3,4-dihydroisoquinolin-2(1H)-yl)methyl]phenol


Mass: 239.312 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H17NO / 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: 3.18 Å3/Da / Density % sol: 61.3 % / Mosaicity: 0.19 °
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 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.34→115.57 Å / Num. obs: 79588 / % possible obs: 96.4 % / Redundancy: 1.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.055 / Rrim(I) all: 0.078 / Net I/σ(I): 6.7 / Num. measured all: 142462 / 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
2.34-2.471.71.07119976117480.4471.0711.5150.697.1
7.4-115.571.80.028441524580.9960.0280.0423.894.5

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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: 2.34→115.57 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 13.293 / SU ML: 0.275 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.278 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2745 3950 5 %RANDOM
Rwork0.212 ---
obs0.2152 75638 96.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 208.37 Å2 / Biso mean: 77.767 Å2 / Biso min: 30.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0 Å20.06 Å2
2---0.01 Å20.07 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 2.34→115.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10033 0 54 157 10244
Biso mean--59.41 77.26 -
Num. residues----1221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01310255
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179729
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.64513789
X-RAY DIFFRACTIONr_angle_other_deg1.321.58422479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.93351210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84521.926597
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.93151974
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9581585
X-RAY DIFFRACTIONr_chiral_restr0.0770.21331
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211477
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022266
X-RAY DIFFRACTIONr_mcbond_it6.3877.9344876
X-RAY DIFFRACTIONr_mcbond_other6.3877.9344876
X-RAY DIFFRACTIONr_mcangle_it9.11211.8846072
LS refinement shellResolution: 2.338→2.399 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 316 -
Rwork0.391 5626 -
all-5942 -
obs--96.79 %

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