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- PDB-2v24: Structure of the human SPRY domain-containing SOCS box protein SSB-4 -

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Basic information

Entry
Database: PDB / ID: 2v24
TitleStructure of the human SPRY domain-containing SOCS box protein SSB-4
ComponentsSPRY DOMAIN-CONTAINING SOCS BOX PROTEIN 4
KeywordsPROTEIN BINDING / PROTEIN-BINDING
Function / homology
Function and homology information


positive regulation of protein polyubiquitination / SCF ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / regulation of circadian rhythm / rhythmic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / intracellular signal transduction ...positive regulation of protein polyubiquitination / SCF ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / regulation of circadian rhythm / rhythmic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / intracellular signal transduction / protein ubiquitination / cytosol
Similarity search - Function
: / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily ...: / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
NICKEL (II) ION / SPRY domain-containing SOCS box protein 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsUppenberg, J. / Bullock, A. / Keates, T. / Savitsky, P. / Pike, A.C.W. / Ugochukwu, E. / Bunkoczi, G. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. ...Uppenberg, J. / Bullock, A. / Keates, T. / Savitsky, P. / Pike, A.C.W. / Ugochukwu, E. / Bunkoczi, G. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A. / Sundstrom, M. / Knapp, S.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural Basis for Par-4 Recognition by the Spry Domain-and Socs Box-Containing Proteins Spsb1, Spsb2, and Spsb4.
Authors: Filippakopoulos, P. / Low, A. / Sharpe, T.D. / Uppenberg, J. / Yao, S. / Kuang, Z. / Savitsky, P. / Lewis, R.S. / Nicholson, S.E. / Norton, R.S. / Bullock, A.
History
DepositionMay 31, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SPRY DOMAIN-CONTAINING SOCS BOX PROTEIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8152
Polymers22,7571
Non-polymers591
Water1,40578
1
A: SPRY DOMAIN-CONTAINING SOCS BOX PROTEIN 4
hetero molecules

A: SPRY DOMAIN-CONTAINING SOCS BOX PROTEIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6314
Polymers45,5132
Non-polymers1172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area1990 Å2
ΔGint-13 kcal/mol
Surface area16350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.220, 104.220, 40.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2054-

HOH

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Components

#1: Protein SPRY DOMAIN-CONTAINING SOCS BOX PROTEIN 4 / SSB-4


Mass: 22756.725 Da / Num. of mol.: 1 / Fragment: RESIDUES 28-233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q96A44
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST TWO RESIDUES REMAIN FROM A CLEAVED HIS6

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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: 2.7 Å3/Da / Density % sol: 55 %
Crystal growpH: 6.5
Details: 0.1 M NACACOD PH6.5, 14.4% PEG10K, 0.16 M CAAC2, 20% GLYCEROL, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.03315
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 15, 2007
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03315 Å / Relative weight: 1
ReflectionResolution: 2.2→45.1 Å / Num. obs: 13208 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.7
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.3.0034refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FNJ

2fnj


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 16.377 / SU ML: 0.212 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26 648 4.9 %RANDOM
Rwork0.209 ---
obs0.212 12517 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.05 Å2
Baniso -1Baniso -2Baniso -3
1--4.05 Å2-2.03 Å20 Å2
2---4.05 Å20 Å2
3---6.08 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1521 0 1 78 1600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211577
X-RAY DIFFRACTIONr_bond_other_d0.0010.021062
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.9412150
X-RAY DIFFRACTIONr_angle_other_deg0.92432565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9795197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.56522.53571
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67315236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6921513
X-RAY DIFFRACTIONr_chiral_restr0.090.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021780
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02339
X-RAY DIFFRACTIONr_nbd_refined0.20.2254
X-RAY DIFFRACTIONr_nbd_other0.1930.21072
X-RAY DIFFRACTIONr_nbtor_refined0.180.2708
X-RAY DIFFRACTIONr_nbtor_other0.0860.2842
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.259
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2970.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2380.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.66331250
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.651564
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.7688707
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.91111585
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: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.342 51
Rwork0.32 909
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.92082.4485-0.35577.8447-0.1393.1909-0.0636-0.1152-0.0699-0.10.13250.07640.2087-0.2197-0.069-0.2827-0.0734-0.0411-0.07610.0023-0.0628-39.402727.6468-4.035
26.44912.1901-1.34857.4962-1.35250.65050.0587-0.5623-0.85670.1894-0.1937-0.88930.1122-0.03450.135-0.1158-0.0786-0.068-0.00870.088-0.0992-30.91823.75551.5035
312.20140.47446.23193.5236-6.110314.6962-0.0637-0.0882-1.262-0.8068-0.6007-1.9184-0.31380.96390.6644-0.0030.0350.111-0.10870.12331.0371-16.281219.1803-2.2732
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 81
2X-RAY DIFFRACTION2A82 - 152
3X-RAY DIFFRACTION2A175 - 233
4X-RAY DIFFRACTION3A157 - 174

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