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- PDB-4atg: TAF6 C-terminal domain from Antonospora locustae -

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Basic information

Entry
Database: PDB / ID: 4atg
TitleTAF6 C-terminal domain from Antonospora locustae
ComponentsTAF6
KeywordsTRANSCRIPTION / TFIID
Function / homology
Function and homology information


SLIK (SAGA-like) complex / SAGA complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / transcription initiation at RNA polymerase II promoter
Similarity search - Function
TAF6, C-terminal HEAT repeat domain / Transcription initiation factor TFIID subunit 6 / TAF6 C-terminal HEAT repeat domain / TAF6, C-terminal HEAT repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Biological speciesANTONOSPORA LOCUSTAE (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.89 Å
AuthorsRomier, C.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: TFIID Taf6-Taf9 Complex Formation Involves the Heat Repeat-Containing C-Terminal Domain of Taf6 and is Modulated by Taf5 Protein.
Authors: Scheer, E. / Delbac, F. / Tora, L. / Moras, D. / Romier, C.
History
DepositionMay 7, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Aug 22, 2012Group: Database references / Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TAF6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0493
Polymers22,6351
Non-polymers4152
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.792, 50.685, 67.293
Angle α, β, γ (deg.)90.00, 100.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TAF6 /


Mass: 22634.561 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 160-355
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ANTONOSPORA LOCUSTAE (fungus) / Plasmid: PNEA-TH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I6L8L5*PLUS
#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNOT IN DATABASES GLY 160 AND SER 161 THROMBIN CLEAVAGE SITE. HIS 162 AND MET 163 ENGINEERED NDE1 CLONING SITE.

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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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growDetails: 0.1 M CHES PH 9.5, 10% (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 17911 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 25.09 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 30.6
Reflection shellResolution: 1.89→1.94 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.8 / % possible all: 99.6

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.89→18.46 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.9311 / SU R Cruickshank DPI: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.138 / SU Rfree Blow DPI: 0.132 / SU Rfree Cruickshank DPI: 0.129
RfactorNum. reflection% reflectionSelection details
Rfree0.2151 915 5.12 %RANDOM
Rwork0.1687 ---
obs0.1711 17887 99.22 %-
Displacement parametersBiso mean: 30.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.8543 Å20 Å2-1.182 Å2
2--0.6527 Å20 Å2
3----1.5069 Å2
Refine analyzeLuzzati coordinate error obs: 0.236 Å
Refinement stepCycle: LAST / Resolution: 1.89→18.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1577 0 26 185 1788
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011661HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.952247HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d622SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes36HARMONIC2
X-RAY DIFFRACTIONt_gen_planes232HARMONIC5
X-RAY DIFFRACTIONt_it1661HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion14.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion220SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2143SEMIHARMONIC4
LS refinement shellResolution: 1.89→2 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2235 151 5.34 %
Rwork0.1786 2676 -
all0.181 2827 -
obs--99.22 %
Refinement TLS params.Method: refined / Origin x: 25.9766 Å / Origin y: 40.0697 Å / Origin z: 15.9232 Å
111213212223313233
T-0.0846 Å20.0216 Å20.0128 Å2--0.014 Å20.0028 Å2---0.0764 Å2
L2.0326 °20.1404 °20.6099 °2-0.9907 °20.7462 °2--1.3196 °2
S-0.0572 Å °-0.4045 Å °-0.0068 Å °0.0516 Å °0.0582 Å °0.008 Å °0.0442 Å °0.037 Å °-0.001 Å °
Refinement TLS groupSelection details: CHAIN A

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