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- PDB-9t2z: Spindlin 1 with crystallization epitope mutations H127D:L128D:T131R -

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Basic information

Entry
Database: PDB / ID: 9t2z
TitleSpindlin 1 with crystallization epitope mutations H127D:L128D:T131R
ComponentsSpindlin-1
KeywordsCELL CYCLE / Crystal epitopes
Function / homology
Function and homology information


transposable element silencing by piRNA-mediated DNA methylation / gamete generation / histone H3K4me3 reader activity / : / histone reader activity / rRNA transcription / positive regulation of Wnt signaling pathway / protein localization to chromatin / meiotic cell cycle / spindle ...transposable element silencing by piRNA-mediated DNA methylation / gamete generation / histone H3K4me3 reader activity / : / histone reader activity / rRNA transcription / positive regulation of Wnt signaling pathway / protein localization to chromatin / meiotic cell cycle / spindle / Wnt signaling pathway / nuclear membrane / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / nucleolus / nucleoplasm / nucleus / cytosol
Similarity search - Function
Spindlin/spermiogenesis-specific protein / Spindlin/spermiogenesis-specific domain superfamily / Spin/Ssty Family
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsFairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Bowesman-Jones, H. / Damerell, D. / Krojer, T. ...Fairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Bowesman-Jones, H. / Damerell, D. / Krojer, T. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Yue, W. / Burgess-Brown, N. / Marsden, B. / von Delft, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
The Structural Genomics Consortium (SGC) Canada
CitationJournal: To Be Published
Title: A fast, parallel method for efficiently exploring crystallization behaviour of large numbers of protein variants.
Authors: Fairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Bowesman-Jones, H. / Damerell, D. / Krojer, T. / Arrowsmith, C.H. / Edwards, A. / ...Authors: Fairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Bowesman-Jones, H. / Damerell, D. / Krojer, T. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Yue, W. / Burgess-Brown, N. / Marsden, B. / von Delft, F.
History
DepositionOct 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spindlin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7214
Polymers25,5351
Non-polymers1863
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint4 kcal/mol
Surface area11980 Å2
Unit cell
Length a, b, c (Å)67.88, 99.91, 45.46
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 25534.742 Da / Num. of mol.: 1 / Mutation: H127D:L128D:T131R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPIN1, OCR, SPIN / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y657
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.02 Å3/Da / Density % sol: 59.25 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M ammonium sulfate 25% PEG3350 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.91→56.28 Å / Num. obs: 24861 / % possible obs: 99.8 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.175 / Net I/σ(I): 3.8
Reflection shellResolution: 1.91→1.96 Å / Rmerge(I) obs: 0.808 / Num. unique obs: 1814

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→49.95 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.875 / SU R Cruickshank DPI: 0.151 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.158 / SU Rfree Blow DPI: 0.146 / SU Rfree Cruickshank DPI: 0.143
RfactorNum. reflection% reflectionSelection details
Rfree0.2879 1342 -RANDOM
Rwork0.2585 ---
obs0.2599 26082 99.2 %-
Displacement parametersBiso mean: 35.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.8675 Å20 Å20 Å2
2---15.5037 Å20 Å2
3---14.6363 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 1.87→49.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1641 0 12 136 1789
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091732HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.952350HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d586SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes297HARMONIC5
X-RAY DIFFRACTIONt_it1732HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion216SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1172SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.68
X-RAY DIFFRACTIONt_other_torsion16.65
LS refinement shellResolution: 1.87→1.88 Å
RfactorNum. reflection% reflection
Rfree0.3122 22 -
Rwork0.3466 --
obs0.3453 522 100 %

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