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- PDB-4ioy: Structure of the Spt16 Middle Domain Reveals Functional Features ... -

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Basic information

Entry
Database: PDB / ID: 4ioy
TitleStructure of the Spt16 Middle Domain Reveals Functional Features of the Histone Chaperone FACT
ComponentsFACT complex subunit SPT16
KeywordsTRANSCRIPTION / Spt16 / FACT / double pleckstrin homology domain / H3-H4 histones
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 / replication fork protection complex / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Pre-transcription Events / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly ...Regulation of TP53 Activity through Phosphorylation / regulation of sister chromatid cohesion / FACT complex / regulation of chromatin organization / nucleosome organization / replication fork protection complex / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Pre-transcription Events / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / nucleosome binding / transcription elongation by RNA polymerase II / DNA-templated DNA replication / nucleosome assembly / chromatin organization / DNA repair / chromatin
Similarity search - Function
PH-domain like - #150 / : / FACT complex subunit SPT16, C-terminal domain / FACT complex subunit Spt16, peptidase M24-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 ...PH-domain like - #150 / : / FACT complex subunit SPT16, C-terminal domain / FACT complex subunit Spt16, peptidase M24-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 / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / FACT complex subunit SPT16
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.945 Å
AuthorsKemble, D.J. / Hill, C.P.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structure of the Spt16 Middle Domain Reveals Functional Features of the Histone Chaperone FACT.
Authors: Kemble, D.J. / Whitby, F.G. / Robinson, H. / McCullough, L.L. / Formosa, T. / Hill, C.P.
History
DepositionJan 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2May 1, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
X: FACT complex subunit SPT16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1622
Polymers33,0671
Non-polymers951
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.978, 133.978, 40.342
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 33066.715 Da / Num. of mol.: 1 / Fragment: Middle Domain (UNP residues 675-958)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SPT16, CDC68, SSF1, YGL207W / Production host: Escherichia coli (E. coli) / References: UniProt: P32558
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 3.16 Å3/Da / Density % sol: 61.09 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M sodium/potassium phosphate, pH 6.0, 0.2 M sodium chloride, 40% PEG400, 10 mM TCEP-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.5418
SYNCHROTRONNSLS X29A20.9792
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV++1IMAGE PLATEJan 1, 2012
ADSC QUANTUM 315r2CCDOct 10, 2012
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1Rosenbaum-Rock double crystal
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.97921
ReflectionResolution: 1.945→30 Å / Num. all: 29648 / Num. obs: 29648 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Rmerge(I) obs: 0.078 / Χ2: 1.034 / Net I/σ(I): 17.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.945-2.0220.51725751.091,284.5
2.02-2.120.40326501.1711,286.9
2.1-2.24.90.50628111.0571,292.8
2.2-2.319.40.45530341.1011,2100
2.31-2.469.80.33830691.0681,2100
2.46-2.6510.50.24230551.0321,2100
2.65-2.9110.80.16130880.9981,2100
2.91-3.3311.30.09330861.0131,2100
3.33-4.211.70.05830730.9921,2100
4.2-3011.60.04732071.0251,2100

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Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.7 / FOM acentric: 0.71 / FOM centric: 0.68 / Reflection: 10440 / Reflection acentric: 9432 / Reflection centric: 1008
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8-38.5710.910.940.84486365121
5-80.860.880.7214141216198
4-50.870.880.7617531573180
3.5-40.780.780.7317621609153
3-3.50.650.650.5931072877230
2.8-30.420.420.4519181792126

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
RESOLVE2.13phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
RefinementMethod to determine structure: SAD / Resolution: 1.945→29.69 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8581 / SU ML: 0.19 / σ(F): 1.34 / Phase error: 21.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1966 1183 3.99 %RANDOM
Rwork0.1766 ---
obs0.1774 29627 96.2 %-
all-29627 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.59 Å2 / Biso mean: 57.4122 Å2 / Biso min: 22.94 Å2
Refinement stepCycle: LAST / Resolution: 1.945→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 5 192 2183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082030
X-RAY DIFFRACTIONf_angle_d1.0862748
X-RAY DIFFRACTIONf_chiral_restr0.077313
X-RAY DIFFRACTIONf_plane_restr0.005355
X-RAY DIFFRACTIONf_dihedral_angle_d16.521771
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.945-2.03390.31191280.26243039316783
2.0339-2.14110.25871310.24263194332588
2.1411-2.27520.2161530.18763632378599
2.2752-2.45080.22041530.1936663819100
2.4508-2.69730.21741550.184136973852100
2.6973-3.08730.23521520.191436823834100
3.0873-3.88830.17731540.167537113865100
3.8883-29.69380.16361570.154938233980100
Refinement TLS params.Method: refined / Origin x: 22.1658 Å / Origin y: 76.3034 Å / Origin z: 19.1313 Å
111213212223313233
T0.2181 Å20.0095 Å2-0.0428 Å2-0.3208 Å20.0178 Å2--0.2904 Å2
L3.0461 °2-1.2197 °20.4681 °2-2.2132 °20.0947 °2--1.9568 °2
S-0.1959 Å °0.0516 Å °0.4995 Å °0.1243 Å °0.0706 Å °-0.4298 Å °-0.1616 Å °0.346 Å °0.0703 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allX677 - 765
2X-RAY DIFFRACTION1allX788 - 941
3X-RAY DIFFRACTION1allX1001
4X-RAY DIFFRACTION1allX1101 - 1292

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