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- PDB-5ip9: Structure of RNA Polymerase II-TFIIF complex -

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Basic information

Entry
Database: PDB / ID: 5ip9
TitleStructure of RNA Polymerase II-TFIIF complex
Components
  • (DNA-directed RNA polymerase II subunit ...Polymerase) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 5
  • PHE-ILE-LYS-ARG-ASP-ARG-MET-ARG-ARG-ASN-PHE-LEU-ARG-MET-ARG
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


promoter clearance from RNA polymerase II promoter / dephosphorylation of RNA polymerase II C-terminal domain / TFIIF-class transcription factor complex binding / regulation of protein serine/threonine phosphatase activity / transcription factor TFIIF complex / transcriptional start site selection at RNA polymerase II promoter / nuclear-transcribed mRNA catabolic process, exonucleolytic / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / mRNA export from nucleus in response to heat stress / RNA polymerase II preinitiation complex assembly ...promoter clearance from RNA polymerase II promoter / dephosphorylation of RNA polymerase II C-terminal domain / TFIIF-class transcription factor complex binding / regulation of protein serine/threonine phosphatase activity / transcription factor TFIIF complex / transcriptional start site selection at RNA polymerase II promoter / nuclear-transcribed mRNA catabolic process, exonucleolytic / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / mRNA export from nucleus in response to heat stress / RNA polymerase II preinitiation complex assembly / RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 1 Promoter / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / RNA polymerase II general transcription initiation factor activity / termination of RNA polymerase II transcription / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Promoter Escape / RNA polymerase II activity / RNA polymerase I activity / protein phosphatase activator activity / RNA Polymerase II Transcription Elongation / positive regulation of translational initiation / Estrogen-dependent gene expression / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of TC-NER Pre-Incision Complex / tRNA transcription by RNA polymerase III / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / transcription by RNA polymerase I / transcription-coupled nucleotide-excision repair / transcription by RNA polymerase III / mRNA cleavage / RNA polymerase I complex / RNA polymerase III complex / translesion synthesis / RNA polymerase II, core complex / transcription elongation from RNA polymerase II promoter / transcription initiation from RNA polymerase II promoter / translation initiation factor binding / positive regulation of transcription elongation from RNA polymerase II promoter / P-body / ribonucleoside binding / transcription by RNA polymerase II / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / transcription, RNA-templated / cytoplasmic stress granule / single-stranded DNA binding / ribosome biogenesis / single-stranded RNA binding / nucleic acid binding / protein dimerization activity / mRNA binding / nucleotide binding / nucleolus / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb7-like, N-terminal domain / Transcription initiation factor IIF, alpha subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription Factor IIF, Rap30/Rap74, interaction / RNA polymerase, Rpb5, N-terminal domain / Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / N-terminal domain of TfIIb - #10 ...RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb7-like, N-terminal domain / Transcription initiation factor IIF, alpha subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription Factor IIF, Rap30/Rap74, interaction / RNA polymerase, Rpb5, N-terminal domain / Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / N-terminal domain of TfIIb - #10 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase II, heptapeptide repeat, eukaryotic / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA polymerase RBP11 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase subunit Rpb4/RPC9 / RNA Polymerase Alpha Subunit; Chain A, domain 2 / RNA polymerase Rpb4 / Growth Hormone; Chain: A; / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / RNA polymerase Rpb7-like , N-terminal / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / Zinc finger TFIIS-type signature. / RNA polymerases N / 8 Kd subunits signature. / RNA polymerases, subunit N, zinc binding site / RNA polymerases N / 8 kDa subunit / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerase subunit RPB10 / RNA polymerase subunit 9 / RNA polymerases M/15 Kd subunit / DNA-directed RNA polymerase, M/15kDa subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase Rpb5, N-terminal domain superfamily / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerase Rpb5, N-terminal domain / RNA polymerase, Rpb5, N-terminal / RNA polymerase, Rpb8 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / DNA-directed RNA polymerase, subunit RPB6 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / RNA polymerases D / 30 to 40 Kd subunits signature. / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase Rpb5, C-terminal domain / RNA polymerase, subunit H/Rpb5, conserved site / : / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase Rpb3/Rpb11 dimerisation domain / : / RPB5-like RNA polymerase subunit superfamily / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Zinc finger TFIIS-type profile. / Transcription factor S-II (TFIIS) / Zinc finger, TFIIS-type / C2C2 Zinc finger / Gyrase A; domain 2 / Ribosomal protein S1-like RNA-binding domain / RNA-binding domain, S1 / S1 RNA binding domain / S1 domain / Homeodomain-like / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb6 / RNA polymerase Rpb6 / RPB6/omega subunit-like superfamily / RNA polymerase, subunit omega/Rpo6/RPB6 / Single Sheet / : / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 2
Similarity search - Domain/homology
DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit RPB7 ...DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / Transcription initiation factor IIF subunit alpha
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsPlaschka, C. / Hantsche, M. / Dienemann, C. / Burzinski, C. / Plitzko, J. / Cramer, P.
CitationJournal: Nature / Year: 2016
Title: Transcription initiation complex structures elucidate DNA opening.
Authors: C Plaschka / M Hantsche / C Dienemann / C Burzinski / J Plitzko / P Cramer /
Abstract: Transcription of eukaryotic protein-coding genes begins with assembly of the RNA polymerase (Pol) II initiation complex and promoter DNA opening. Here we report cryo-electron microscopy (cryo-EM) ...Transcription of eukaryotic protein-coding genes begins with assembly of the RNA polymerase (Pol) II initiation complex and promoter DNA opening. Here we report cryo-electron microscopy (cryo-EM) structures of yeast initiation complexes containing closed and open DNA at resolutions of 8.8 Å and 3.6 Å, respectively. DNA is positioned and retained over the Pol II cleft by a network of interactions between the TATA-box-binding protein TBP and transcription factors TFIIA, TFIIB, TFIIE, and TFIIF. DNA opening occurs around the tip of the Pol II clamp and the TFIIE 'extended winged helix' domain, and can occur in the absence of TFIIH. Loading of the DNA template strand into the active centre may be facilitated by movements of obstructing protein elements triggered by allosteric binding of the TFIIE 'E-ribbon' domain. The results suggest a unified model for transcription initiation with a key event, the trapping of open promoter DNA by extended protein-protein and protein-DNA contacts.
History
DepositionMar 9, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Jun 8, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase II subunit RPB1
B: DNA-directed RNA polymerase II subunit RPB2
C: DNA-directed RNA polymerase II subunit RPB3
D: DNA-directed RNA polymerase II subunit RPB4
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
G: DNA-directed RNA polymerase II subunit RPB7
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
Q: PHE-ILE-LYS-ARG-ASP-ARG-MET-ARG-ARG-ASN-PHE-LEU-ARG-MET-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)498,98322
Polymers498,43613
Non-polymers5489
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area66670 Å2
ΔGint-326 kcal/mol
Surface area151010 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)222.820, 392.730, 283.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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DNA-directed RNA polymerase II subunit ... , 7 types, 7 molecules ABCDGIK

#1: Protein DNA-directed RNA polymerase II subunit RPB1 / Polymerase / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II ...RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit B220


Mass: 191690.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P04050, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase II subunit RPB2 / Polymerase / RNA polymerase II subunit 2 / B150 / DNA-directed RNA polymerase II 140 kDa polypeptide


Mass: 138806.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P08518, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase II subunit RPB3 / Polymerase / RNA polymerase II subunit B3 / B44.5 / DNA-directed RNA polymerase II 45 kDa polypeptide


Mass: 29921.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P16370
#4: Protein DNA-directed RNA polymerase II subunit RPB4 / Polymerase / RNA polymerase II subunit B4 / B32 / DNA-directed RNA polymerase II 32 kDa polypeptide


Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P20433
#7: Protein DNA-directed RNA polymerase II subunit RPB7 / Polymerase / RNA polymerase II subunit B7 / B16


Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P34087
#9: Protein DNA-directed RNA polymerase II subunit RPB9 / Polymerase / RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA- ...RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA-directed RNA polymerase II subunit 9


Mass: 13942.714 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P27999
#11: Protein DNA-directed RNA polymerase II subunit RPB11 / Polymerase / RNA polymerase II subunit B11 / B13.6 / DNA-directed RNA polymerase II 13.6 kDa polypeptide


Mass: 13113.989 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38902

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DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL

#5: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase / RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 ...RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 kDa polypeptide


Mass: 24985.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P20434
#6: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerase / RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 ...RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 kDa polypeptide


Mass: 10046.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P20435
#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase / RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I / and III 14.5 kDa polypeptide


Mass: 16394.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P20436
#10: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerase / RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I / and III 8.3 kDa polypeptide


Mass: 7647.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P22139
#12: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha


Mass: 5252.261 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P40422

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Protein/peptide , 1 types, 1 molecules Q

#13: Protein/peptide PHE-ILE-LYS-ARG-ASP-ARG-MET-ARG-ARG-ASN-PHE-LEU-ARG-MET-ARG


Mass: 2102.603 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P41895*PLUS

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Non-polymers , 2 types, 9 molecules

#14: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#15: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 6.22 Å3/Da / Density % sol: 80.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: peg 6000, sodium acetate, ammonium acetate, hepes, tcep

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.91889 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91889 Å / Relative weight: 1
ReflectionResolution: 3.45→50 Å / Num. obs: 112721 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 99.89 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.206 / Net I/σ(I): 9.19
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.45-3.544.0110.631100
3.54-3.642.8270.87199.9
3.64-3.741.8811.31100
3.74-3.861.4371.691100
3.86-3.981.0312.371100
3.98-4.120.6783.451100
4.12-4.280.4894.81100
4.28-4.450.3356.771100
4.45-4.650.2718.331100
4.65-4.880.229.961100
4.88-5.140.20310.731100
5.14-5.450.18711.181100
5.45-5.830.16812.231100
5.83-6.30.14414.231100
6.3-6.90.11316.811100
6.9-7.710.0821.02199.9
7.71-8.910.05626.721100
8.91-10.910.04434.46199.9
10.91-15.430.03838.35199.9
15.430.03242.41195.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER-TNT2.10.2refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PO2
Resolution: 3.9→48.93 Å / Cor.coef. Fo:Fc: 0.9248 / Cor.coef. Fo:Fc free: 0.8954 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU Rfree Blow DPI: 0.383
RfactorNum. reflection% reflectionSelection details
Rfree0.1937 2265 2.01 %RANDOM
Rwork0.1622 ---
obs0.1628 112717 99.97 %-
Displacement parametersBiso max: 300 Å2 / Biso mean: 130.08 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-3.8406 Å20 Å20 Å2
2--25.5238 Å20 Å2
3----29.3644 Å2
Refine analyzeLuzzati coordinate error obs: 0.385 Å
Refinement stepCycle: final / Resolution: 3.9→48.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31330 0 9 0 31339
Biso mean--124.4 --
Num. residues----3950
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d11507SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes859HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4553HARMONIC5
X-RAY DIFFRACTIONt_it31891HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion4206SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance38HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact37326SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d31891HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg43050HARMONIC21.26
X-RAY DIFFRACTIONt_omega_torsion2.74
X-RAY DIFFRACTIONt_other_torsion23.94
LS refinement shellResolution: 3.9→4 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2915 155 1.88 %
Rwork0.2272 8085 -
all0.2283 8240 -
obs--99.94 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
18.68561.4480.55322.3303-0.35122.1122-0.01150.6308-0.77180.016-0.0786-0.0890.4862-0.31550.0901-0.3162-0.04260.13010.19650.0098-0.353398.481331.7277-37.8527
21.10780.74080.28383.7726-0.76811.6918-0.03650.35780.3214-0.0055-0.17160.2615-0.129-0.19630.2081-0.48780.1722-0.05050.1720.3727-0.068991.513359.4881-40.8573
30.31860.2160.48410.4974-0.18081.27150.03880.09010.15920.2445-0.0949-0.0970.10540.07770.0561-0.177-0.02910.0095-0.07290.0643-0.0512125.82936.63345.1955
41.2563-0.7988-0.35392.6085-0.40750-0.07090.07120.44470.7812-0.15230.1204-0.21450.12020.22320.1958-0.06950.2098-0.2727-0.29320.0029103.53269.365825.3714
52.24220.68990.67660.960.09980.1930.1942-0.04910.33810.1459-0.1143-0.18950.0129-0.0452-0.0799-0.41-0.08990.0864-0.19520.15950.3081140.07266.8794-2.6252
65.7121-3.82180.38721.7538-0.65150.5359-0.2432-0.15230.7280.11760.1192-0.57190.0082-0.0680.124-0.49630.07820.0295-0.4866-0.17370.9119101.954104.570.365
70.12090.11280.74181.29230.30740.34460.09230.3360.6415-0.0812-0.1882-0.05390.1441-0.08590.096-0.37960.06980.1375-0.0720.19850.2408118.98759.1296-18.4193
80.4066-1.2007-0.05730.4765-0.26800.0649-0.1617-0.12580.09110.11571.0227-0.072-0.1231-0.1806-0.43490.05020.3111-0.19780.0360.714666.765644.520910.4976
94.67740.36921.77984.9706-1.03922.0022-0.10210.1098-0.2219-0.16740.22880.24960.0008-0.0229-0.1267-0.48990.23080.1678-0.4411-0.17860.536566.646383.6992-5.8316
101.7099-0.25991.187100.29721.0085-0.12320.20220.3413-0.19470.2860.7447-0.06110.2323-0.1628-0.20160.05910.181-0.21320.03050.355375.072651.69421.5771
110.0124-1.81580.52950.6168-1.03871.1777-0.1397-0.28390.39090.391-0.08380.40430.0397-0.20540.2236-0.19710.26220.4559-0.1886-0.15080.443869.355168.351326.2079
120-1.1113-0.34321.2727-0.6990.2832-0.0844-0.15170.15270.39670.24430.13310.0109-0.0367-0.1599-0.0265-0.02920.3595-0.147-0.12-0.062793.035142.36323.3411
130.07310.8861.73462.93930.61063.957-0.22680.0563-0.0141-0.6760.51070.6559-0.01220.415-0.28390.0393-0.23220.0848-0.22290.0202-0.012786.738317.0139-0.4611
140.4005-0.0610.00010.1217-0.21421.29610.04580.12070.23930.1750.05810.1170.172-0.0242-0.1039-0.07260.02010.1315-0.08960.0028-0.1789108.54138.3982.0771
151.2011-0.00130.11191.1303-0.08130.1989-0.0697-0.297-0.24620.75720.05070.05660.20650.05930.01910.3289-0.00440.1892-0.03720.1795-0.4998110.55816.446236.2838
160.1493-0.0894-0.11831.0362-0.1024.3608-0.0490.3411-0.03560.18510.1054-0.02640.06130.563-0.0564-0.40820.15760.07230.3883-0.092-0.3327135.86529.8736-65.5017
171.2184-0.27910.02763.86080.1160.34380.05790.18030.5267-0.4658-0.1345-0.1336-0.05530.13980.0766-0.3138-0.06980.0802-0.34430.44410.5299126.93592.7723-25.3168
181.369-0.10840.09435.9984-0.54832.53070.05110.130.15670.1530.054-0.51060.20680.2566-0.1051-0.42510.0760.0670.10920.1417-0.0852139.69338.7219-19.8766
190.21330.16141.39870.97291.55365.29450.00420.0553-0.24240.13710.09150.11470.46640.3482-0.0957-0.27750.24640.13660.24780.0089-0.1799126.30723.3184-59.6886
202.28311.64831.44263.93-1.0011.4855-0.1879-0.32750.41720.5085-0.1378-0.6469-0.24890.29690.3257-0.0316-0.3091-0.45590.0424-0.066-0.1398152.24952.35436.373
210.6906-1.51061.47771.4295-2.21162.1602-0.15310.15080.41430.7644-0.05110.4612-0.02180.18340.20410.01170.27390.2978-0.3725-0.26680.651376.888499.312614.1705
223.66681.0445-0.60380.72650.41830.5738-0.03650.09650.29370.61010.08520.28830.11690.2386-0.04870.27220.05260.4208-0.13380.0531-0.268791.164825.841437.5209
231.12610.53620.58082.0994-1.35930-0.06620.3737-0.25480.4154-0.1259-0.31960.11450.2030.19220.10540.1733-0.0821-0.01920.1129-0.3388131.96317.398128.2003
241.46961.44491.26523.22281.18663.54590.12140.0711-0.41330.4871-0.26331.39150.5542-0.0450.1419-0.1156-0.25340.2418-0.25570.22060.457776.35199.64979.1671
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|3 - A|81 }A3 - 81
2X-RAY DIFFRACTION2{ A|82 - A|323 }A82 - 323
3X-RAY DIFFRACTION3{ A|324 - A|659 }A324 - 659
4X-RAY DIFFRACTION4{ A|660 - A|831 }A660 - 831
5X-RAY DIFFRACTION5{ A|832 - A|1127 }A832 - 1127
6X-RAY DIFFRACTION6{ A|1128 - A|1329 }A1128 - 1329
7X-RAY DIFFRACTION7{ A|1330 - A|1454 }A1330 - 1454
8X-RAY DIFFRACTION8{ B|20 - B|234 }B20 - 234
9X-RAY DIFFRACTION9{ B|235 - B|392 }B235 - 392
10X-RAY DIFFRACTION10{ B|393 - B|539 }B393 - 539
11X-RAY DIFFRACTION11{ B|540 - B|735 }B540 - 735
12X-RAY DIFFRACTION12{ B|736 - B|841 }B736 - 841
13X-RAY DIFFRACTION13{ B|842 - B|974 }B842 - 974
14X-RAY DIFFRACTION14{ B|975 - B|1224 }B975 - 1224
15X-RAY DIFFRACTION15{ C|3 - C|268 }C3 - 268
16X-RAY DIFFRACTION16{ D|4 - D|221 }D4 - 221
17X-RAY DIFFRACTION17{ E|2 - E|215 }E2 - 215
18X-RAY DIFFRACTION18{ F|72 - F|155 }F72 - 155
19X-RAY DIFFRACTION19{ G|1 - G|171 }G1 - 171
20X-RAY DIFFRACTION20{ H|2 - H|146 }H2 - 146
21X-RAY DIFFRACTION21{ I|2 - I|120 }I2 - 120
22X-RAY DIFFRACTION22{ J|1 - J|65 }J1 - 65
23X-RAY DIFFRACTION23{ K|2 - K|114 }K2 - 114
24X-RAY DIFFRACTION24{ L|25 - L|70 }L25 - 70

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