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- PDB-3bit: Crystal structure of yeast Spt16 N-terminal Domain -

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Basic information

Entry
Database: PDB / ID: 3bit
TitleCrystal structure of yeast Spt16 N-terminal Domain
ComponentsFACT complex subunit SPT16
KeywordsTRANSCRIPTION / pita-bread / aminopeptidase / chromatin / replication / FACT / Activator / Chromosomal protein / DNA damage / DNA repair / DNA replication / Nucleus / Phosphoprotein / Repressor / Transcription regulation
Function / homology
Function and homology information


Regulation of TP53 Activity through Phosphorylation / regulation of sister chromatid cohesion / FACT complex / regulation of chromatin organization / nucleosome organization / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Pre-transcription Events / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / transcription elongation by RNA polymerase II ...Regulation of TP53 Activity through Phosphorylation / regulation of sister chromatid cohesion / FACT complex / regulation of chromatin organization / nucleosome organization / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Pre-transcription Events / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / transcription elongation by RNA polymerase II / DNA-templated DNA replication / nucleosome assembly / chromatin organization / DNA repair / chromatin
Similarity search - Function
FACT complex subunit Spt16, peptidase M24-like domain / : / FACT complex subunit SPT16, C-terminal domain / : / FACT complex subunit SPT16 PH-like domain / FACT complex subunit Spt16 domain / FACT complex subunit (SPT16/CDC68) / FACT complex subunit (SPT16/CDC68) / FACT complex subunit Spt16, N-terminal lobe domain / FACT complex subunit Spt16 ...FACT complex subunit Spt16, peptidase M24-like domain / : / FACT complex subunit SPT16, C-terminal domain / : / FACT complex subunit SPT16 PH-like domain / FACT complex subunit Spt16 domain / FACT complex subunit (SPT16/CDC68) / FACT complex subunit (SPT16/CDC68) / FACT complex subunit Spt16, N-terminal lobe domain / FACT complex subunit Spt16 / FACT complex subunit SPT16 N-terminal lobe domain / FACT complex subunit SPT16 N-terminal lobe domain / Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domain / Histone chaperone Rttp106-like, middle domain / Histone chaperone Rttp106-like / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / PH-like domain superfamily / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / FACT complex subunit SPT16
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsVanDemark, A.P. / Xin, H. / McCullough, L. / Rawlins, R. / Bentley, S. / Heroux, A. / David, S.J. / Hill, C.P. / Formosa, T.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural and functional analysis of the Spt16p N-terminal domain reveals overlapping roles of yFACT subunits.
Authors: VanDemark, A.P. / Xin, H. / McCullough, L. / Rawlins, R. / Bentley, S. / Heroux, A. / Stillman, D.J. / Hill, C.P. / Formosa, T.
History
DepositionNov 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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_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

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Assembly

Deposited unit
A: FACT complex subunit SPT16
B: FACT complex subunit SPT16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,70310
Polymers104,2342
Non-polymers4688
Water18,6281034
1
A: FACT complex subunit SPT16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2664
Polymers52,1171
Non-polymers1493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FACT complex subunit SPT16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4366
Polymers52,1171
Non-polymers3195
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.683, 144.635, 88.513
Angle α, β, γ (deg.)90.00, 101.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FACT complex subunit SPT16 / Facilitates chromatin transcription complex subunit SPT16 / Suppressor of Ty protein 16 / Cell ...Facilitates chromatin transcription complex subunit SPT16 / Suppressor of Ty protein 16 / Cell division control protein 68


Mass: 52117.109 Da / Num. of mol.: 2 / Fragment: residues 1-451
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SPT16, CDC68, SSF1 / Plasmid: pKA8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon+(RIL) / References: UniProt: P32558
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1034 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 278 K / Method: vapor diffusion / pH: 4.5
Details: 35% PEG 300, 200mM NaCl, 100mM Sodium Acetate, pH 4.5, vapor diffusion, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.97791 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 5, 2004
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97791 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 78683 / Num. obs: 73962 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.097 / Χ2: 1.307 / Net I/σ(I): 8.1
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.455 / Num. unique all: 5482 / Χ2: 0.921 / % possible all: 70

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
HKL-2000data reduction
PHASESphasing
RefinementResolution: 1.9→39.88 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.77 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 3741 5.1 %RANDOM
Rwork0.167 ---
obs0.17 73959 93.81 %-
all-78683 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.647 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å20.26 Å2
2---0.79 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7144 0 22 1034 8200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227593
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.96710317
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9885948
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.72325.698358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.384151386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4081526
X-RAY DIFFRACTIONr_chiral_restr0.0990.21140
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025782
X-RAY DIFFRACTIONr_nbd_refined0.2050.23826
X-RAY DIFFRACTIONr_nbtor_refined0.3040.25306
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2818
X-RAY DIFFRACTIONr_metal_ion_refined0.110.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.296
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.257
X-RAY DIFFRACTIONr_mcbond_it0.5821.54630
X-RAY DIFFRACTIONr_mcangle_it1.04427573
X-RAY DIFFRACTIONr_scbond_it1.97933056
X-RAY DIFFRACTIONr_scangle_it3.064.52744
LS refinement shellResolution: 1.9→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 210 -
Rwork0.219 3640 -
all-3850 -
obs--65.76 %

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