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- PDB-3nfq: Crystal structure of the conserved central domain of yeast Spn1/Iws1 -

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Basic information

Entry
Database: PDB / ID: 3nfq
TitleCrystal structure of the conserved central domain of yeast Spn1/Iws1
ComponentsTranscription factor IWS1
KeywordsTRANSCRIPTION / Spn1 / RNA polymerase II
Function / homology
Function and homology information


regulation of transcription elongation by RNA polymerase II / poly(A)+ mRNA export from nucleus / RNA polymerase II complex binding / RNA polymerase II-specific DNA-binding transcription factor binding / regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 / TFIIS helical bundle-like domain / Transcription factor IIS, N-terminal / TFIIS N-terminal domain profile. / Transcription Elongation Factor S-II; Chain A / TFIIS/LEDGF domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription factor SPN1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsStargell, L.A. / Luger, K.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: The Transcription Factor Spn1 Regulates Gene Expression via a Highly Conserved Novel Structural Motif.
Authors: Pujari, V. / Radebaugh, C.A. / Chodaparambil, J.V. / Muthurajan, U.M. / Almeida, A.R. / Fischbeck, J.A. / Luger, K. / Stargell, L.A.
History
DepositionJun 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription factor IWS1
B: Transcription factor IWS1


Theoretical massNumber of molelcules
Total (without water)39,3692
Polymers39,3692
Non-polymers00
Water7,458414
1
A: Transcription factor IWS1


Theoretical massNumber of molelcules
Total (without water)19,6841
Polymers19,6841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transcription factor IWS1


Theoretical massNumber of molelcules
Total (without water)19,6841
Polymers19,6841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.6, 67.8, 76.0
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transcription factor IWS1 / Interacts with SPT6 protein 1 / Suppresses postrecruitment functions protein 1


Mass: 19684.271 Da / Num. of mol.: 2 / Fragment: mini-Spn1 conserved domain, residues 141-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: FT5 / Gene: IWS1, SPN1, YPR133C / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLysS / References: UniProt: Q06505
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: potassium chloride, sodium thiocyanate, PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9791, 0.9793, 0.9716
DetectorDetector: CCD
RadiationMonochromator: Rosenbaum-rock / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97931
30.97161
ReflectionResolution: 1.85→39.6 Å / Num. obs: 28618 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Redundancy: 3.02 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 12.1
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.01 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2813 / Rsym value: 0.396 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SOLVEphasing
REFMAC5refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.85→33.15 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.988 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.158
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26456 1458 5.1 %RANDOM
Rwork0.20347 ---
obs0.20658 27160 100 %-
all-28618 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.686 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å20 Å20 Å2
2---0.43 Å20 Å2
3---1.55 Å2
Refinement stepCycle: LAST / Resolution: 1.85→33.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2304 0 0 414 2718
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222333
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.712.0053156
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4385288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77325.6797
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.77115467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9221513
X-RAY DIFFRACTIONr_chiral_restr0.1070.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021659
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.21209
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21647
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.240.2335
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.264
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2490.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4311.51490
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.28822355
X-RAY DIFFRACTIONr_scbond_it3.5153931
X-RAY DIFFRACTIONr_scangle_it5.6144.5801
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 98 -
Rwork0.282 1989 -
obs--100 %

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