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- PDB-1wm3: Crystal structure of human SUMO-2 protein -

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Basic information

Entry
Database: PDB / ID: 1wm3
TitleCrystal structure of human SUMO-2 protein
ComponentsUbiquitin-like protein SMT3B
KeywordsPROTEIN TRANSPORT / ubiquitin fold / half-open barrel / two helices
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 / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / 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 / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / SUMOylation of transcription factors / protein sumoylation / SUMOylation of DNA damage response and repair proteins / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / 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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsHuang, W.-C. / Ko, T.-P. / Li, S.S.-L. / Wang, A.H.-J.
CitationJournal: Eur.J.Biochem. / Year: 2004
Title: Crystal structures of the human SUMO-2 protein at 1.6 A and 1.2 A resolution: implication on the functional differences of SUMO proteins
Authors: Huang, W.-C. / Ko, T.-P. / Li, S.S.-L. / Wang, A.H.-J.
History
DepositionJul 2, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-like protein SMT3B


Theoretical massNumber of molelcules
Total (without water)8,3631
Polymers8,3631
Non-polymers00
Water2,288127
1
A: Ubiquitin-like protein SMT3B

A: Ubiquitin-like protein SMT3B

A: Ubiquitin-like protein SMT3B


Theoretical massNumber of molelcules
Total (without water)25,0883
Polymers25,0883
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)74.964, 74.964, 33.231
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-201-

HOH

21A-202-

HOH

31A-203-

HOH

41A-204-

HOH

51A-205-

HOH

DetailsThe protein functions as monomer, but in this crystal structure it may form a trimer, via the 3-fold axis.

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Components

#1: Protein Ubiquitin-like protein SMT3B / SUMO-2 / small ubiquitin-like modifier / Sentrin 2 / HSMT3


Mass: 8362.512 Da / Num. of mol.: 1 / Fragment: no N-terminal arm(residues 17-88)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: brain / Gene: SUMO-2 / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61956
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 1.81 Å3/Da / Density % sol: 31.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 40% PEG600, 0.1M CHES, 0.1M Na-HEPES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL17B2 / Wavelength: 1.0717 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 7, 2003 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0717 Å / Relative weight: 1
ReflectionResolution: 1.2→20 Å / Num. all: 21786 / Num. obs: 21781 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.49 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 39.6
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 5.24 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2190 / % possible all: 99.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1WM2

1wm2


Resolution: 1.2→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.185 1014 -RANDOM
Rwork0.119 ---
all0.124 21786 --
obs0.122 20948 96.2 %-
Displacement parametersBiso mean: 26.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.013 Å
Refinement stepCycle: LAST / Resolution: 1.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms584 0 0 127 711
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONo_angle_deg2.3
LS refinement shellResolution: 1.2→1.24 Å / Rfactor Rfree error: 0.013
RfactorNum. reflection% reflection
Rfree0.239 90 -
Rwork0.217 --
obs-1924 88 %

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