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- PDB-3qht: Crystal Structure of the Monobody ySMB-1 bound to yeast SUMO -

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Basic information

Entry
Database: PDB / ID: 3qht
TitleCrystal Structure of the Monobody ySMB-1 bound to yeast SUMO
Components
  • Monobody ySMB-1
  • Ubiquitin-like protein SMT3
KeywordsDE NOVO PROTEIN / Fibronectin Type III / yeast small ubiquitin-like modifier / SMT3
Function / homology
Function and homology information


SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMOylation of SUMOylation proteins / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring / SUMOylation of DNA damage response and repair proteins ...SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMOylation of SUMOylation proteins / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring / SUMOylation of DNA damage response and repair proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA replication proteins / SUMOylation of chromatin organization proteins / ubiquitin-like protein ligase binding / protein sumoylation / condensed nuclear chromosome / protein tag activity / identical protein binding / 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 family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Immunoglobulins ...Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Immunoglobulins / Roll / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-like protein SMT3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
artificial gene (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKoide, S. / Gilbreth, R.N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Isoform-specific monobody inhibitors of small ubiquitin-related modifiers engineered using structure-guided library design.
Authors: Gilbreth, R.N. / Truong, K. / Madu, I. / Koide, A. / Wojcik, J.B. / Li, N.S. / Piccirilli, J.A. / Chen, Y. / Koide, S.
History
DepositionJan 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq / 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.db_align_beg / _struct_ref_seq.db_align_end / _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: Ubiquitin-like protein SMT3
B: Ubiquitin-like protein SMT3
C: Monobody ySMB-1
D: Monobody ySMB-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,93412
Polymers43,1984
Non-polymers7378
Water1,53185
1
A: Ubiquitin-like protein SMT3
C: Monobody ySMB-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,33610
Polymers21,5992
Non-polymers7378
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-5 kcal/mol
Surface area9280 Å2
MethodPISA
2
B: Ubiquitin-like protein SMT3
D: Monobody ySMB-1


Theoretical massNumber of molelcules
Total (without water)21,5992
Polymers21,5992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-6 kcal/mol
Surface area8990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.637, 175.462, 52.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Ubiquitin-like protein SMT3 / yeast small ubiquitin-like modifier (SUMO)


Mass: 11204.536 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SMT3, YDR510W, D9719.15 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12306
#2: Protein Monobody ySMB-1


Mass: 10394.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 3.2 Å3/Da / Density % sol: 61.55 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 8
Details: 14% PEG8000, 16% glycerol, pH 8.0, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 18, 2009
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 22586 / Num. obs: 22586 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 18.9
Reflection shellResolution: 2.395→2.457 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 2.15 / % possible all: 96.29

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Processing

Software
NameVersionClassification
MD2data collection
MAR345data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1FNA AND 2EKE

1fna

2eke


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.896 / SU B: 14.399 / SU ML: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.287 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27158 1151 5.1 %RANDOM
Rwork0.2231 ---
all0.22558 21341 --
obs0.22558 21341 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.816 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.7 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2666 0 48 85 2799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222777
X-RAY DIFFRACTIONr_angle_refined_deg1.8641.9783759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8065336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.57523.636121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.32315449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3281516
X-RAY DIFFRACTIONr_chiral_restr0.160.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022084
X-RAY DIFFRACTIONr_nbd_refined0.2320.21185
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21898
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2142
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.270.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.212
X-RAY DIFFRACTIONr_mcbond_it1.1071.51733
X-RAY DIFFRACTIONr_mcangle_it1.92322752
X-RAY DIFFRACTIONr_scbond_it2.56831203
X-RAY DIFFRACTIONr_scangle_it3.9184.51007
LS refinement shellResolution: 2.395→2.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 81 -
Rwork0.247 1450 -
obs--96.29 %

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