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- PDB-2ns2: Crystal Structure of Spindlin1 -

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Basic information

Entry
Database: PDB / ID: 2ns2
TitleCrystal Structure of Spindlin1
ComponentsSpindlin-1
KeywordsCELL CYCLE / Beta Barrel / Repeat Domains
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
PHOSPHATE ION / Spindlin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.2 Å
AuthorsZhao, Q. / Qin, L. / Jiang, F. / Wu, B. / Yue, W. / Xu, F. / Rong, Z. / Yuan, H. / Xie, X. / Gao, Y. ...Zhao, Q. / Qin, L. / Jiang, F. / Wu, B. / Yue, W. / Xu, F. / Rong, Z. / Yuan, H. / Xie, X. / Gao, Y. / Bai, C. / Bartlam, M.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structure of human spindlin1. Tandem tudor-like domains for cell cycle regulation
Authors: Zhao, Q. / Qin, L. / Jiang, F. / Wu, B. / Yue, W. / Xu, F. / Rong, Z. / Yuan, H. / Xie, X. / Gao, Y. / Bai, C. / Bartlam, M. / Pei, X. / Rao, Z.
History
DepositionNov 2, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)55,2444
Polymers55,0552
Non-polymers1902
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-20 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.793, 84.876, 136.567
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 27527.250 Da / Num. of mol.: 2 / Fragment: residues 1-237 (26-262)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPIN, OCR, SPIN1 / Plasmid: pGEX-6p-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y657
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.15 Å3/Da / Density % sol: 42.68 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Ammonium Sulfate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 20, 2004
RadiationMonochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 25041 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 17.8 % / Biso Wilson estimate: 40.2 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 17.4 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 7.9 / Num. unique all: 2468 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→30.38 Å / Isotropic thermal model: Isotropic / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2453 -RANDOM
Rwork0.225 ---
all0.236 24901 --
obs0.231 24611 98.8 %-
Displacement parametersBiso mean: 49.5 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3023 0 10 241 3274
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0085
X-RAY DIFFRACTIONc_angle_deg1.78

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