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- PDB-3mp8: Crystal structure of Sgf29 tudor domain -

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Basic information

Entry
Database: PDB / ID: 3mp8
TitleCrystal structure of Sgf29 tudor domain
ComponentsMaltose-binding periplasmic protein,LINKER,SAGA-associated factor 29
KeywordsHISTONE BINDING PROTEIN / Histone / Tudor Domain / SAGA
Function / homology
Function and homology information


ADA complex / SAGA complex localization to transcription regulatory region / SLIK (SAGA-like) complex / SAGA complex / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity ...ADA complex / SAGA complex localization to transcription regulatory region / SLIK (SAGA-like) complex / SAGA complex / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / methylated histone binding / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / protein localization / outer membrane-bounded periplasmic space / chromatin organization / periplasmic space / DNA damage response / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / membrane / nucleus
Similarity search - Function
SGF29 tudor-like domain / SAGA-associated factor 29 / : / : / SGF29 tudor-like domain / SGF29 C-terminal domain profile. / SH3 type barrels. - #140 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. ...SGF29 tudor-like domain / SAGA-associated factor 29 / : / : / SGF29 tudor-like domain / SGF29 C-terminal domain profile. / SH3 type barrels. - #140 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / SH3 type barrels. / Roll / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / 4-(HYDROXYMETHYL)BENZAMIDINE / ACETIC ACID / Maltose/maltodextrin-binding periplasmic protein / SAGA-associated factor 29
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
unidentified (others)
Saccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsLi, J. / Wu, M. / Ruan, J. / Zang, J.
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
DepositionApr 26, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 12, 2013Group: Database references
Revision 1.3Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.value
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein,LINKER,SAGA-associated factor 29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,71526
Polymers57,5221
Non-polymers2,19325
Water7,855436
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.760, 95.100, 114.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Maltose-binding periplasmic protein,LINKER,SAGA-associated factor 29 / MBP / Sgf29


Mass: 57521.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: chimera of Maltose-binding periplasmic protein, SAGA-associated factor 29
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) unidentified (others), (gene. exp.) Saccharomyces cerevisiae S288C (yeast)
Strain: K12, S288c / Gene: malE, SGF29 / Plasmid: pET23b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AEX9, UniProt: P25554
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 6 types, 460 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#7: Chemical ChemComp-4BZ / 4-(HYDROXYMETHYL)BENZAMIDINE


Mass: 150.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10N2O
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 2.0M ammonium sulfate, 0.1M sodium acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. all: 42425 / Num. obs: 40594 / % possible obs: 95.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.084 / Net I/σ(I): 16.5
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 4 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 4.8 / Num. unique all: 1642 / Rsym value: 0.258 / % possible all: 79.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HSJ

1hsj


Resolution: 1.92→41.14 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.22 / WRfactor Rwork: 0.193 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.878 / SU R Cruickshank DPI: 0.166 / SU Rfree: 0.149 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1158 3 %RANDOM
Rwork0.19 ---
obs0.191 37279 94.83 %-
all-39311 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 72.47 Å2 / Biso mean: 23.248 Å2 / Biso min: 4 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å20 Å20 Å2
2---1.48 Å20 Å2
3----0.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.92→41.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3992 0 135 436 4563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224245
X-RAY DIFFRACTIONr_angle_refined_deg0.9861.9965764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8815526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34525.137183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55915690
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2231517
X-RAY DIFFRACTIONr_chiral_restr0.0620.2618
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213207
LS refinement shellResolution: 1.917→1.967 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 64 -
Rwork0.229 2078 -
all-2142 -
obs-2142 90.49 %

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