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- PDB-3mew: Crystal structure of Novel Tudor domain-containing protein SGF29 -

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Basic information

Entry
Database: PDB / ID: 3mew
TitleCrystal structure of Novel Tudor domain-containing protein SGF29
ComponentsSAGA-associated factor 29 homolog
KeywordsTRANSCRIPTION / Structural Genomics Consortium / SGC / Nucleus / Transcription regulation / Chromosomal protein / DNA-binding / Nucleosome core
Function / homology
Function and homology information


SAGA-type complex / establishment of protein localization to chromatin / ATAC complex / SAGA complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of RNA splicing / regulation of embryonic development / regulation of DNA repair ...SAGA-type complex / establishment of protein localization to chromatin / ATAC complex / SAGA complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of RNA splicing / regulation of embryonic development / regulation of DNA repair / methylated histone binding / response to endoplasmic reticulum stress / transcription initiation-coupled chromatin remodeling / mitotic spindle / HATs acetylate histones / regulation of cell cycle / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm
Similarity search - Function
SGF29 tudor-like domain / SAGA-associated factor 29 / : / : / SGF29 tudor-like domain / SGF29 C-terminal domain profile. / SH3 type barrels. - #140 / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
SAGA-associated factor 29
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsXu, C. / Bian, C.B. / Lam, R. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / Bochkarev, A. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Embo J. / Year: 2011
Title: Sgf29 binds histone H3K4me2/3 and is required for SAGA complex recruitment and histone H3 acetylation.
Authors: Bian, C. / Xu, C. / Ruan, J. / Lee, K.K. / Burke, T.L. / Tempel, W. / Barsyte, D. / Li, J. / Wu, M. / Zhou, B.O. / Fleharty, B.E. / Paulson, A. / Allali-Hassani, A. / Zhou, J.Q. / Mer, G. / ...Authors: Bian, C. / Xu, C. / Ruan, J. / Lee, K.K. / Burke, T.L. / Tempel, W. / Barsyte, D. / Li, J. / Wu, M. / Zhou, B.O. / Fleharty, B.E. / Paulson, A. / Allali-Hassani, A. / Zhou, J.Q. / Mer, G. / Grant, P.A. / Workman, J.L. / Zang, J. / Min, J.
History
DepositionMar 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Database references
Revision 1.3Sep 6, 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: SAGA-associated factor 29 homolog


Theoretical massNumber of molelcules
Total (without water)17,8141
Polymers17,8141
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.623, 41.424, 52.324
Angle α, β, γ (deg.)90.000, 121.430, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SAGA-associated factor 29 homolog / Coiled-coil domain-containing protein 101


Mass: 17813.990 Da / Num. of mol.: 1 / Fragment: UNP Residues 115-287
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCDC101, SGF29 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q96ES7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.4 Å3/Da / Density % sol: 48.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20-28% PEG3350, 0.1M Bis-Tris pH 5.5, vapor diffusion, Sitting drop, temperature 291K, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.92→44.65 Å / Num. all: 13104 / Num. obs: 12062 / % possible obs: 92.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.0381 / Net I/σ(I): 37.9
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.119 / Mean I/σ(I) obs: 15.4 / % possible all: 88.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ME9

3me9


Resolution: 1.92→44.65 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.551 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.235 587 4.9 %RANDOM
Rwork0.199 11477 --
obs0.201 12062 92.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 66.14 Å2 / Biso mean: 31.39 Å2 / Biso min: 16.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å2-1.48 Å2
2--0.12 Å20 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 1.92→44.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1245 0 0 84 1329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221281
X-RAY DIFFRACTIONr_angle_refined_deg2.0011.9761753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9935155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.8562460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07715196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.103159
X-RAY DIFFRACTIONr_chiral_restr0.1340.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0221006
X-RAY DIFFRACTIONr_mcbond_it1.3711.5793
X-RAY DIFFRACTIONr_mcangle_it2.35421290
X-RAY DIFFRACTIONr_scbond_it3.7083488
X-RAY DIFFRACTIONr_scangle_it6.1184.5463
LS refinement shellResolution: 1.92→1.971 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 40 -
Rwork0.232 811 -
all-851 -
obs--87.73 %

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