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- PDB-5jsj: Crystal structure of Spindlin1 bound to compound EML631 -

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Basic information

Entry
Database: PDB / ID: 5jsj
TitleCrystal structure of Spindlin1 bound to compound EML631
ComponentsSpindlin-1
KeywordsCELL CYCLE / Tudor domain
Function / homology
Function and homology information


gamete generation / rRNA transcription / positive regulation of Wnt signaling pathway / methylated histone binding / meiotic cell cycle / Wnt signaling pathway / spindle / chromatin organization / nuclear membrane / regulation of DNA-templated transcription ...gamete generation / rRNA transcription / positive regulation of Wnt signaling pathway / methylated histone binding / meiotic cell cycle / Wnt signaling pathway / spindle / chromatin organization / nuclear membrane / regulation of DNA-templated transcription / nucleolus / positive regulation of DNA-templated transcription / nucleoplasm / nucleus / cytosol
Similarity search - Function
Spindlin/Ssty / Spindlin/spermiogenesis-specific protein / Spindlin/spermiogenesis-specific domain superfamily / Spin/Ssty Family / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Chem-6PD / Spindlin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.348 Å
AuthorsSu, X. / Li, H.
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Developing Spindlin1 small-molecule inhibitors by using protein microarrays
Authors: Bae, N. / Viviano, M. / Su, X. / Lv, J. / Cheng, D. / Sagum, C. / Castellano, S. / Bai, X. / Johnson, C. / Khalil, M.I. / Shen, J. / Chen, K. / Li, H. / Sbardella, G. / Bedford, M.T.
History
DepositionMay 8, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spindlin-1
B: Spindlin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4857
Polymers51,0192
Non-polymers1,4655
Water1,51384
1
A: Spindlin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2544
Polymers25,5101
Non-polymers7453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area11340 Å2
MethodPISA
2
B: Spindlin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2303
Polymers25,5101
Non-polymers7202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area11670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.790, 123.827, 49.663
Angle α, β, γ (deg.)90.000, 92.220, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Spindlin-1 / Ovarian cancer-related protein / Spindlin1


Mass: 25509.748 Da / Num. of mol.: 2 / Fragment: Spin/Ssty Repeats, UNP residues 50-262
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPIN1, OCR, SPIN / Plasmid: RSFDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y657
#2: Chemical ChemComp-6PD / [4-(2-pyrrolidin-1-ylethyl)piperidin-1-yl]-[4-[4-(2-pyrrolidin-1-ylethyl)piperidin-1-yl]carbonyl-3-[[4-(pyrrolidin-1-ylmethoxy)phenyl]amino]phenyl]methanone


Mass: 684.953 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H60N6O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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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: 2.58 Å3/Da / Density % sol: 52.27 % / Mosaicity: 0.464 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2M MgCl2, 0.1M HepesNa, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9778 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2015 / Details: mirrors
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 21323 / % possible obs: 98.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 43.6 Å2 / Rmerge(I) obs: 0.092 / Χ2: 1.329 / Net I/av σ(I): 22.05 / Net I/σ(I): 6.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.35-2.45.30.318189.9
2.4-2.465.30.283195.3
2.46-2.535.40.269199
2.53-2.615.40.242199.6
2.61-2.695.40.2121100
2.69-2.795.20.193199.9
2.79-2.95.20.169199.9
2.9-3.035.70.144199.8
3.03-3.195.70.1271100
3.19-3.395.60.1161100
3.39-3.655.30.1021100
3.65-4.025.50.088199.9
4.02-4.65.60.075199.9
4.6-5.795.20.069199.9
5.79-505.50.067199.6

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Processing

Software
NameVersionClassification
PHENIXdev_2689: ???refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
MOLREPphasing
RefinementResolution: 2.348→42.758 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 33.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 1057 4.98 %Random selection
Rwork0.1987 20185 --
obs0.2013 21242 98.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.98 Å2 / Biso mean: 56.4348 Å2 / Biso min: 32.48 Å2
Refinement stepCycle: final / Resolution: 2.348→42.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3166 0 103 84 3353
Biso mean--51.93 52 -
Num. residues----391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093352
X-RAY DIFFRACTIONf_angle_d0.9464537
X-RAY DIFFRACTIONf_chiral_restr0.052472
X-RAY DIFFRACTIONf_plane_restr0.006571
X-RAY DIFFRACTIONf_dihedral_angle_d16.7741991
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3479-2.45480.32551150.26782311242691
2.4548-2.58420.32941190.25452544266399
2.5842-2.74610.29711250.24712547267299
2.7461-2.95810.33391590.238225352694100
2.9581-3.25560.29421250.217325592684100
3.2556-3.72650.2441190.201525552674100
3.7265-4.69410.19571570.171225522709100
4.6941-42.76490.23921380.17472582272099

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