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- PDB-5a1h: Crystal structure of human Spindlin3 -

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Basic information

Entry
Database: PDB / ID: 5a1h
TitleCrystal structure of human Spindlin3
ComponentsSPINDLIN-3
KeywordsCELL CYCLE
Function / homologySpindlin/spermiogenesis-specific protein / Spindlin/spermiogenesis-specific domain superfamily / Spin/Ssty Family / gamete generation / : / regulation of DNA-templated transcription / nucleoplasm / cytosol / Spindlin-3
Function and homology information
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSrikannathasan, V. / Gileadi, C. / Johansson, C. / Shrestha, L. / Tallon, R. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of Human Spindlin3
Authors: Srikannathasan, V. / Gileadi, C. / Johansson, C. / Shrestha, L. / Tallon, R. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U.
History
DepositionApr 30, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SPINDLIN-3
B: SPINDLIN-3
C: SPINDLIN-3
D: SPINDLIN-3


Theoretical massNumber of molelcules
Total (without water)102,1954
Polymers102,1954
Non-polymers00
Water10,791599
1
A: SPINDLIN-3


Theoretical massNumber of molelcules
Total (without water)25,5491
Polymers25,5491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SPINDLIN-3


Theoretical massNumber of molelcules
Total (without water)25,5491
Polymers25,5491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SPINDLIN-3


Theoretical massNumber of molelcules
Total (without water)25,5491
Polymers25,5491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: SPINDLIN-3


Theoretical massNumber of molelcules
Total (without water)25,5491
Polymers25,5491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.580, 129.400, 129.480
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-3 / SPINDLIN4 / SPINDLIN-LIKE PROTEIN 3 / SPIN-3


Mass: 25548.750 Da / Num. of mol.: 4 / Fragment: RESIDUES 45-258 IS PEPTIDE BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q5JUX0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 599 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsHISTIDINE TAG CLEAVED, THE NUMBERING START AT 47 CHAIN A, B AND D, CHAIN C STARTS AT 46. AT THE C- ...HISTIDINE TAG CLEAVED, THE NUMBERING START AT 47 CHAIN A, B AND D, CHAIN C STARTS AT 46. AT THE C-TERMINAL CHAINS ABCD HAVE EXTRA RESIDUES FROM THE EXPRESSION VECTOR

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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: 2.48 Å3/Da / Density % sol: 50.4 % / Description: TWINNED DATA
Crystal growpH: 9 / Details: 0.1M TRIS PH 8.4, 38% PEG3350

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.502
11-H, L, K20.498
ReflectionResolution: 2→2.11 Å / Num. obs: 67153 / % possible obs: 99.7 % / Observed criterion σ(I): 3.1 / Redundancy: 7.6 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 11.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.1 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4Iphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NS2

4ns2


Resolution: 2→26.14 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.913 / SU B: 2.247 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21244 3267 4.9 %RANDOM
Rwork0.17164 ---
obs0.17358 63818 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.525 Å2
Baniso -1Baniso -2Baniso -3
1--7.56 Å20 Å20 Å2
2--0.3 Å20 Å2
3---7.26 Å2
Refinement stepCycle: LAST / Resolution: 2→26.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5911 0 0 599 6510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196072
X-RAY DIFFRACTIONr_bond_other_d0.0120.025607
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.958231
X-RAY DIFFRACTIONr_angle_other_deg1.872312870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2415732
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.44724.099283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65215988
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3811527
X-RAY DIFFRACTIONr_chiral_restr0.0820.2892
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026809
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021402
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0862.3092967
X-RAY DIFFRACTIONr_mcbond_other2.0852.3092966
X-RAY DIFFRACTIONr_mcangle_it3.2143.4463686
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3652.4023105
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 244 -
Rwork0.247 4539 -
obs--96.98 %

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