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- PDB-2a26: Crystal structure of the N-terminal, dimerization domain of Siah ... -

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Basic information

Entry
Database: PDB / ID: 2a26
TitleCrystal structure of the N-terminal, dimerization domain of Siah Interacting Protein
ComponentsCalcyclin-binding protein
KeywordsAPOPTOSIS / helical hairpin / dimerization
Function / homology
Function and homology information


beta-catenin destruction complex / S100 protein binding / SCF ubiquitin ligase complex / nuclear envelope lumen / cellular response to leukemia inhibitory factor / tubulin binding / heart development / protein domain specific binding / ubiquitin protein ligase binding / protein homodimerization activity ...beta-catenin destruction complex / S100 protein binding / SCF ubiquitin ligase complex / nuclear envelope lumen / cellular response to leukemia inhibitory factor / tubulin binding / heart development / protein domain specific binding / ubiquitin protein ligase binding / protein homodimerization activity / extracellular exosome / nucleoplasm / nucleus / cytosol
Similarity search - Function
Siah interacting protein, N-terminal / Calcyclin-binding protein, N-terminal / Calcyclin-binding Protein, CS domain / Siah interacting protein, N terminal / UVR domain / SGS domain / SGS domain / SGS domain profile. / DNA Excision Repair, Uvrb; Chain A / CS domain ...Siah interacting protein, N-terminal / Calcyclin-binding protein, N-terminal / Calcyclin-binding Protein, CS domain / Siah interacting protein, N terminal / UVR domain / SGS domain / SGS domain / SGS domain profile. / DNA Excision Repair, Uvrb; Chain A / CS domain / CS domain / CS domain profile. / HSP20-like chaperone / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Calcyclin-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.2 Å
AuthorsSantelli, E. / Leone, M. / Li, C. / Fukushima, T. / Preece, N.E. / Olson, A.J. / Ely, K.R. / Reed, J.C. / Pellecchia, M. / Liddington, R.C. / Matsuzawa, S.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural Analysis of Siah1-Siah-interacting Protein Interactions and Insights into the Assembly of an E3 Ligase Multiprotein Complex
Authors: Santelli, E. / Leone, M. / Li, C. / Fukushima, T. / Preece, N.E. / Olson, A.J. / Ely, K.R. / Reed, J.C. / Pellecchia, M. / Liddington, R.C. / Matsuzawa, S.
History
DepositionJun 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / 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

Downloads & links

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Assembly

Deposited unit
A: Calcyclin-binding protein
B: Calcyclin-binding protein
C: Calcyclin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7475
Polymers17,4293
Non-polymers3172
Water4,143230
1
A: Calcyclin-binding protein
B: Calcyclin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9374
Polymers11,6192
Non-polymers3172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-7 kcal/mol
Surface area6790 Å2
MethodPISA
2
C: Calcyclin-binding protein

C: Calcyclin-binding protein


Theoretical massNumber of molelcules
Total (without water)11,6192
Polymers11,6192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
3
A: Calcyclin-binding protein
B: Calcyclin-binding protein
C: Calcyclin-binding protein
hetero molecules

A: Calcyclin-binding protein
B: Calcyclin-binding protein
C: Calcyclin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,49310
Polymers34,8586
Non-polymers6354
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area9750 Å2
ΔGint-38 kcal/mol
Surface area15910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.793, 152.609, 36.988
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-340-

HOH

21C-120-

HOH

31C-129-

HOH

41C-133-

HOH

51C-134-

HOH

DetailsThe biological assembly is a dimer comprising chains A and B. A second dimeric biological assembly is generated by chain C by applying the transformations x, y, z and -x, y, 1/2-z

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Components

#1: Protein/peptide Calcyclin-binding protein / CacyBP / hCacyBP / Siah-interacting protein / S100A6-binding protein / PNAS-107


Mass: 5809.732 Da / Num. of mol.: 3 / Fragment: N-terminal domain (residues 1-47)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CACYBP, S100A6BP, SIP / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HB71
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID / CAPS (buffer)


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.35 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: ammonium sulphate, CAPS, lithium sulphate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-110.826533
SYNCHROTRONSSRL BL9-220.91833, 0.83208, 0.92014, 0.95369
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDMar 17, 2002
ADSC QUANTUM 42CCDMar 30, 2002
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.8265331
20.918331
30.832081
40.920141
50.953691
ReflectionResolution: 1.2→50 Å / Num. obs: 50772 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -4 / Redundancy: 8.3 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 65
Reflection shellResolution: 1.2→1.22 Å / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.2→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 0.517 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19833 2568 5.1 %RANDOM
Rwork0.17366 ---
obs0.17489 50769 96.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.758 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å20 Å2
2---0.38 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1244 0 19 230 1493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211205
X-RAY DIFFRACTIONr_angle_refined_deg1.9362.0031607
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0435150
X-RAY DIFFRACTIONr_chiral_restr0.110.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02803
X-RAY DIFFRACTIONr_nbd_refined0.2360.2572
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2113
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.238
X-RAY DIFFRACTIONr_mcbond_it1.8281.5752
X-RAY DIFFRACTIONr_mcangle_it2.8592.51222
X-RAY DIFFRACTIONr_scbond_it3.4093.5453
X-RAY DIFFRACTIONr_scangle_it4.774.5385
X-RAY DIFFRACTIONr_rigid_bond_restr1.6921205
X-RAY DIFFRACTIONr_sphericity_free5.4212230
X-RAY DIFFRACTIONr_sphericity_bonded5.33321203
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.245 149
Rwork0.192 2735

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