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- PDB-3psf: Crystal Structure of the Spt6 core domain from Saccharomyces cere... -

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Basic information

Entry
Database: PDB / ID: 3psf
TitleCrystal Structure of the Spt6 core domain from Saccharomyces cerevisiae, Form Spt6(236-1259)
ComponentsTranscription elongation factor SPT6
KeywordsTRANSCRIPTION / Transcription Elongation / Nucleus
Function / homology
Function and homology information


carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / transcription antitermination factor activity, DNA binding / regulation of transcriptional start site selection at RNA polymerase II promoter / regulation of mRNA 3'-end processing / nucleosome organization / poly(A)+ mRNA export from nucleus / transcription elongation-coupled chromatin remodeling / nucleosome binding / transcription elongation factor complex / transcription antitermination ...carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / transcription antitermination factor activity, DNA binding / regulation of transcriptional start site selection at RNA polymerase II promoter / regulation of mRNA 3'-end processing / nucleosome organization / poly(A)+ mRNA export from nucleus / transcription elongation-coupled chromatin remodeling / nucleosome binding / transcription elongation factor complex / transcription antitermination / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / euchromatin / nucleosome assembly / chromatin organization / histone binding / chromatin remodeling / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleus
Similarity search - Function
Spt6, Death-like domain / Spt6, helix-hairpin-helix domain / RuvA domain 2-like / Tex N-terminal region-like / Tex N-terminal region-like / YqgF/RNase H-like domain / : / Spt6, S1/OB domain / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. ...Spt6, Death-like domain / Spt6, helix-hairpin-helix domain / RuvA domain 2-like / Tex N-terminal region-like / Tex N-terminal region-like / YqgF/RNase H-like domain / : / Spt6, S1/OB domain / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. / Spt6 acidic, N-terminal domain / Helix-turn-helix DNA-binding domain of Spt6 / Transcription elongation factor Spt6, YqgF domain / Transcription elongation factor Spt6, helix-hairpin-helix motif / Spt6, SH2 domain, C terminus / Acidic N-terminal SPT6 / Helix-hairpin-helix motif / Holliday-junction resolvase-like of SPT6 / Helix-turn-helix DNA-binding domain of SPT6 / Tex-like protein, HTH domain superfamily / Tex-like domain superfamily / Spt6, Death-like domain / Transcription elongation factor Spt6 / Spt6, SH2 domain, N terminus / Spt6, SH2 domain / SH2 domain / YqgF/RNase H-like domain superfamily / RuvA domain 2-like / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A / Ribonuclease H-like superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Transcription elongation factor SPT6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.59 Å
AuthorsClose, D. / Hill, C.P.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal structures of the S. cerevisiae Spt6 core and C-terminal tandem SH2 domain.
Authors: Close, D. / Johnson, S.J. / Sdano, M.A. / McDonald, S.M. / Robinson, H. / Formosa, T. / Hill, C.P.
History
DepositionDec 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription elongation factor SPT6


Theoretical massNumber of molelcules
Total (without water)119,2021
Polymers119,2021
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.052, 116.176, 117.348
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transcription elongation factor SPT6 / Chromatin elongation factor SPT6


Mass: 119201.672 Da / Num. of mol.: 1 / Fragment: unp residues 235-1259
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: CRE2, G6169, SPT6, SSN20, YGR116W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P23615
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 3.29 Å3/Da / Density % sol: 62.61 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 50mM Mg(HCO2)2, 10% Glycerol, 1.0 M NDSB-256 , pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 286K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97922 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 8, 2008
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 2.59→32.32 Å / Num. all: 48005 / Num. obs: 48005 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 65.05 Å2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å32.32 Å
Translation2.5 Å32.32 Å

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Processing

Software
NameVersionClassificationNB
PHASER1.3.3phasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→32.32 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.36 / σ(F): 0 / Phase error: 30.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2651 1918 4 %
Rwork0.2238 --
obs0.2255 48003 96.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.591 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso max: 346.88 Å2 / Biso mean: 103.5701 Å2 / Biso min: 48.47 Å2
Baniso -1Baniso -2Baniso -3
1--11.0338 Å2-0 Å20 Å2
2---1.9606 Å2-0 Å2
3---12.9943 Å2
Refinement stepCycle: LAST / Resolution: 2.59→32.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6741 0 0 48 6789
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066869
X-RAY DIFFRACTIONf_angle_d0.8959278
X-RAY DIFFRACTIONf_chiral_restr0.0491021
X-RAY DIFFRACTIONf_plane_restr0.0041211
X-RAY DIFFRACTIONf_dihedral_angle_d14.0222618
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5868-2.67920.34961650.28734020418585
2.6792-2.78640.31371900.27394320451092
2.7864-2.91310.30691870.24694479466695
2.9131-3.06660.33291820.25954545472796
3.0666-3.25860.31181880.25654675486398
3.2586-3.50990.28882000.23714705490599
3.5099-3.86260.28652090.220547594968100
3.8626-4.42030.22211900.185947924982100
4.4203-5.56450.22631920.20148445036100
5.5645-32.32290.25852150.23224946516199
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6068-0.347-0.50381.19190.13182.9414-0.1015-0.0924-0.1381-0.1269-0.3278-0.196-0.03790.33090.44450.3194-0.0385-0.00340.59310.32110.9057-12.235625.456-13.9305
22.51560.68830.00160.63360.87782.7253-0.21170.2835-1.7346-0.1240.2214-0.51420.78170.05560.13190.8647-0.15850.28640.50260.10551.18410.573226.7328-36.8391
32.3590.9938-0.97610.3584-0.54692.2046-0.7656-0.1204-0.7384-0.45980.1234-0.73381.09230.05180.66540.9421-0.10870.32020.64570.12020.792323.645642.5512-48.8711
40.2592-0.83040.3364.0329-0.1640.7974-0.0974-0.0372-0.4654-0.37370.24721.04650.0974-0.3467-0.19070.6245-0.11490.08970.81020.25720.917-2.751952.3191-32.5409
50.9657-1.64190.26133.1342-0.87770.4478-0.2979-0.4332-0.3852-0.29260.93241.39970.306-0.6775-0.53590.7178-0.1827-0.04040.64420.46481.4024-10.640654.7841-27.9774
61.0805-0.8432-0.92980.35960.42641.1426-0.2938-0.0735-0.0341-0.23030.1261-0.09270.21060.02580.07870.4919-0.0722-0.06280.39830.22210.67492.14747.9255-30.031
71.53360.65040.23370.7460.84040.90910.0539-0.22570.4107-0.1307-0.160.0101-0.1324-0.07360.02190.52520.11650.14970.71410.22741.0503-56.454547.6201-8.1494
82.612-1.75420.09661.1587-0.18331.58950.59040.66980.3388-0.1552-0.0512-0.4316-0.062-0.4136-0.35640.47050.04310.09410.78560.2560.6443-47.797540.4525-14.7106
93.4432-0.25320.27942.3742-0.90051.26680.1512-0.0958-0.2961-0.1618-0.19330.11020.1198-0.2803-0.00370.3577-0.0264-0.00210.54950.11340.6988-31.654622.6481-11.727
100.3229-0.5987-0.0461.94480.65022.9806-0.3573-0.5316-0.8308-0.0845-0.03790.96080.1228-1.03880.11910.4651-0.1086-0.08881.08110.48961.0332-27.807514.700617.56
113.7061-2.50261.46591.9734-2.36010.6813-0.0317-0.76480.18610.29590.1314-0.1629-0.3512-0.2773-0.14030.5498-0.0243-0.04360.5860.10680.7617-27.137934.44311.6803
122.61210.9165-0.47492.2995-0.6240.5499-0.7182-0.87430.06550.32850.4750.2405-0.0264-0.09280.23150.78250.15520.15940.62520.12170.7259-14.563872.8986-37.1048
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 298:429)A298 - 429
2X-RAY DIFFRACTION2(chain A and resid 430:505)A430 - 505
3X-RAY DIFFRACTION3(chain A and resid 506:578)A506 - 578
4X-RAY DIFFRACTION4(chain A and resid 579:622)A579 - 622
5X-RAY DIFFRACTION5(chain A and resid 623:657)A623 - 657
6X-RAY DIFFRACTION6(chain A and resid 658:740)A658 - 740
7X-RAY DIFFRACTION7(chain A and resid 741:837)A741 - 837
8X-RAY DIFFRACTION8(chain A and resid 838:885)A838 - 885
9X-RAY DIFFRACTION9(chain A and resid 886:1026)A886 - 1026
10X-RAY DIFFRACTION10(chain A and resid 1027:1076)A1027 - 1076
11X-RAY DIFFRACTION11(chain A and resid 1077:1128)A1077 - 1128
12X-RAY DIFFRACTION12(chain A and resid 1219:1248)A1219 - 1248

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