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- PDB-4bkg: crystal structure of human diSUMO-2 -

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Basic information

Entry
Database: PDB / ID: 4bkg
Titlecrystal structure of human diSUMO-2
ComponentsSMALL UBIQUITIN-RELATED MODIFIER 2
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / SUMO transferase activity / ubiquitin-like protein ligase binding / SUMOylation of transcription factors / protein sumoylation ...SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / SUMO transferase activity / ubiquitin-like protein ligase binding / SUMOylation of transcription factors / protein sumoylation / SUMOylation of DNA replication proteins / postsynaptic cytosol / presynaptic cytosol / SUMOylation of DNA damage response and repair proteins / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / hippocampal mossy fiber to CA3 synapse / Regulation of endogenous retroelements by KRAB-ZFP proteins / GABA-ergic synapse / SUMOylation of intracellular receptors / PML body / Formation of Incision Complex in GG-NER / protein tag activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Processing of DNA double-strand break ends / ubiquitin protein ligase binding / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus
Similarity search - Function
Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Small ubiquitin-related modifier 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsKeusekotten, K. / Bade, V.N. / Meyer-Teschendorf, K. / Sriramachandran, A. / Fischer-Schrader, K. / Krause, A. / Horst, C. / Hofmann, K. / Dohmen, R.J. / Praefcke, G.J.K.
CitationJournal: Biochem.J. / Year: 2014
Title: Multivalent Interactions of the Sumo-Interaction Motifs in the Ring-Finger Protein 4 (Rnf4) Determine the Specificity for Chains of the Small Ubiquitin-Related Modifier (Sumo).
Authors: Keusekotten, K. / Bade, V.N. / Meyer-Teschendorf, K. / Sriramachandran, A.M. / Fischer-Schrader, K. / Krause, A. / Horst, C. / Schwarz, G. / Hofmann, K. / Dohmen, R.J. / Praefcke, G.J.
History
DepositionApr 25, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Sep 21, 2016Group: Source and taxonomy
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Jun 6, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_wavelength_list / _diffrn_source.source
Revision 1.5Dec 20, 2023Group: 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

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Assembly

Deposited unit
A: SMALL UBIQUITIN-RELATED MODIFIER 2


Theoretical massNumber of molelcules
Total (without water)19,1851
Polymers19,1851
Non-polymers00
Water48627
1
A: SMALL UBIQUITIN-RELATED MODIFIER 2

A: SMALL UBIQUITIN-RELATED MODIFIER 2


Theoretical massNumber of molelcules
Total (without water)38,3712
Polymers38,3712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_444-x+y-1/3,-x-2/3,z-2/31
MethodPQS
Unit cell
Length a, b, c (Å)74.988, 74.988, 33.267
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsTHE PROTEIN CHAIN IS SEGMENTED INTO DIFFERENT ASUS VIA A CRYSTALLOGRAPHIC SYMMETRY AXIS. THUS THE DIMERIC ASSEMBLY IS ACTUALLY A MONOMER IN WHICH THE HALVES ARE RELATED BY SYMMETRY AND LINKED VIA AN UNOBSERVED LINKER

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Components

#1: Protein SMALL UBIQUITIN-RELATED MODIFIER 2 / SUMO-2 / HSMT3 / SMT3 HOMOLOG 2 / SUMO-3 / SENTRIN-2 / SMT3A / UBIQUITIN-LIKE PROTEIN SMT3A / SMALL ...SUMO-2 / HSMT3 / SMT3 HOMOLOG 2 / SUMO-3 / SENTRIN-2 / SMT3A / UBIQUITIN-LIKE PROTEIN SMT3A / SMALL UBIQUITIN-LIKE MODIFER 2


Mass: 19185.377 Da / Num. of mol.: 1 / Fragment: SUMO-2DELTAN11, RESIDUES 12-93
Source method: isolated from a genetically manipulated source
Details: LINEAR FUSION-PROTEIN OF 2 SUMO2-DELTAN11 FRAGMENTS, WHICH ARE PRESENT IN DIFFERENT ASU, RELATED VIA A CRYSTALLOGRAPHIC SYMMETRY AXIS
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-4T2 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P61956
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 1.89 Å3/Da / Density % sol: 34.91 % / Description: NONE
Crystal growpH: 8
Details: 0.1 M TRIS/HCL PH 8.0, 28% PEG 350MME,0.05% DIOXANE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION NOVA / Wavelength: 1.5406 / Wavelength: 1.5406 Å
DetectorType: OXFORD DIFFRACTION / Detector: CCD / Date: Jan 24, 2013 / Details: NOVA
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.1→23.24 Å / Num. obs: 3842 / % possible obs: 94.8 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.5
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.9 / % possible all: 73.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WM3

1wm3


Resolution: 2.11→19.76 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.918 / SU B: 5.426 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.287 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 17-89 MAKE UP THE CONTENT OF THE ASU. RESIDUES 101-173 ARE IDENTICAL TO RESIDUES 17-89, AND SEGMENTED INTO DIFFERENT ASU VIA A ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 17-89 MAKE UP THE CONTENT OF THE ASU. RESIDUES 101-173 ARE IDENTICAL TO RESIDUES 17-89, AND SEGMENTED INTO DIFFERENT ASU VIA A CRYSTALLOGRAPHIC SYMMETRY AXIS. THE GAP OF APPROX. 14 A BETWEEN THE C-TERMINUS OF A MOLECULE IN A ASU TO THE N-TERMINUS OF A SYMMETRY-RELATED MOLECULE IN THE ADJACENT ASU CAN BE FILLED BY 11 RESIDUES FROM THE LINKER (90-100) WHICH ARE DELOCALIZED. THE TERMINAL RESIDUES 10-16 AND 174-177 ARE FLEXIBLE AND NOT OBSERVED IN THE CRYSTAL STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.23074 171 4.5 %RANDOM
Rwork0.17872 ---
obs0.18092 3668 94.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.678 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0.39 Å20 Å2
2---0.39 Å20 Å2
3---1.28 Å2
Refinement stepCycle: LAST / Resolution: 2.11→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms585 0 0 27 612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.019612
X-RAY DIFFRACTIONr_bond_other_d0.0010.02588
X-RAY DIFFRACTIONr_angle_refined_deg1.8791.957824
X-RAY DIFFRACTIONr_angle_other_deg0.91731357
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.814576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97825.31232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.80515118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.625154
X-RAY DIFFRACTIONr_chiral_restr0.1040.289
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021706
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02143
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 2.106→2.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.195 7 -
Rwork0.244 217 -
obs--72.73 %

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