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

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Basic information

Entry
Database: PDB / ID: 5qss
TitlePanDDA analysis group deposition -- Crystal Structure of human STAG1 in complex with Z33452282
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
N-(2-hydroxy-4-methylphenyl)-2-methylbenzamide / Cohesin subunit SA-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 3.08 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)105,7473
Polymers105,5062
Non-polymers2411
Water2,738152
1
A: Cohesin subunit SA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9942
Polymers52,7531
Non-polymers2411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 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
Unit cell
Length a, b, c (Å)155.347, 167.209, 48.177
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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-O2P / N-(2-hydroxy-4-methylphenyl)-2-methylbenzamide


Mass: 241.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H15NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.97 Å3/Da / Density % sol: 58.52 % / 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: Apr 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 3.08→113.84 Å / Num. obs: 24203 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.08 / Rrim(I) all: 0.2 / Net I/σ(I): 5.4 / Num. measured all: 151922 / Scaling rejects: 175
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
3.08-3.166.40.8491132017710.7680.3640.9251.7100
13.77-113.845.60.06419053420.9940.0310.07114.399.7

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Phasing

PhasingMethod: molecular replacement

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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: 3.08→113.81 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.924 / SU B: 37.477 / SU ML: 0.579 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.515 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2956 1215 5 %RANDOM
Rwork0.2393 ---
obs0.2422 22929 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 211.72 Å2 / Biso mean: 96.009 Å2 / Biso min: 39.85 Å2
Baniso -1Baniso -2Baniso -3
1--9.13 Å20 Å20 Å2
2---3.37 Å20 Å2
3---12.5 Å2
Refinement stepCycle: final / Resolution: 3.08→113.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6922 0 18 152 7092
Biso mean--64.01 73.39 -
Num. residues----860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0137062
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176624
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.639540
X-RAY DIFFRACTIONr_angle_other_deg1.1441.57415388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2725850
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.3823.733367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.963151311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5661532
X-RAY DIFFRACTIONr_chiral_restr0.0570.2928
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027724
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021392
X-RAY DIFFRACTIONr_mcbond_it7.35410.2983430
X-RAY DIFFRACTIONr_mcbond_other7.3510.2973429
X-RAY DIFFRACTIONr_mcangle_it11.6915.3974270
LS refinement shellResolution: 3.079→3.159 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 75 -
Rwork0.439 1674 -
all-1749 -
obs--99.21 %

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