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- PDB-9t31: Spindlin family member 4 with crystallization epitope mutations G... -

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Basic information

Entry
Database: PDB / ID: 9t31
TitleSpindlin family member 4 with crystallization epitope mutations G129S:H131E
ComponentsSpindlin-4
KeywordsPEPTIDE BINDING PROTEIN / crystal epitopes
Function / homology
Function and homology information


gamete generation / histone H3K4me3 reader activity / : / positive regulation of canonical Wnt signaling pathway / negative regulation of cell population proliferation / regulation of DNA-templated transcription / chromatin / nucleoplasm / nucleus / cytoplasm / 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: 2.04 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 5, 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-4
B: Spindlin-4


Theoretical massNumber of molelcules
Total (without water)49,8072
Polymers49,8072
Non-polymers00
Water2,738152
1
A: Spindlin-4


Theoretical massNumber of molelcules
Total (without water)24,9031
Polymers24,9031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Spindlin-4


Theoretical massNumber of molelcules
Total (without water)24,9031
Polymers24,9031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.78, 61.95, 84.9
Angle α, β, γ (deg.)90, 96.86, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Spindlin-4


Mass: 24903.338 Da / Num. of mol.: 2 / Mutation: G129S:H131E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPIN4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q56A73
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
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: 2.82 Å3/Da / Density % sol: 56.37 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25% PEG3350 0.1M tris pH 8.5

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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 PILATUS 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: 2.01→53.58 Å / Num. obs: 36696 / % possible obs: 98.4 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 6.6
Reflection shellResolution: 2.01→2.06 Å / Rmerge(I) obs: 0.706 / Num. unique obs: 2726

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→53.4 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.859 / SU R Cruickshank DPI: 0.323 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.208 / SU Rfree Blow DPI: 0.187 / SU Rfree Cruickshank DPI: 0.189
RfactorNum. reflection% reflectionSelection details
Rfree0.3005 1703 -RANDOM
Rwork0.2629 ---
obs0.2648 34990 98.5 %-
Displacement parametersBiso mean: 44.91 Å2
Baniso -1Baniso -2Baniso -3
1--20.6551 Å20 Å28.0332 Å2
2--15.7469 Å20 Å2
3---4.9082 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.04→53.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3148 0 0 152 3300
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086377HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9811527HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1843SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes988HARMONIC5
X-RAY DIFFRACTIONt_it3242HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion418SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4488SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.26
X-RAY DIFFRACTIONt_other_torsion16.24
LS refinement shellResolution: 2.04→2.05 Å
RfactorNum. reflection% reflection
Rfree0.3798 35 -
Rwork0.3805 --
obs0.3804 700 99.57 %

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