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- PDB-3s17: RNA Polymerase II Initiation Complex with a 9-nt RNA -

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Basic information

Entry
Database: PDB / ID: 3s17
TitleRNA Polymerase II Initiation Complex with a 9-nt RNA
Components
  • (DNA-directed RNA polymerase II subunit ...) x 5
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • DNA (5'-D(*CP*TP*AP*CP*CP*GP*AP*TP*AP*AP*GP*CP*AP*GP*AP*CP*GP*AP*TP*CP*CP*TP*CP*TP*CP*GP*AP*TP*G)-3')
  • RNA (5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*G)-3')
KeywordsTRANSCRIPTION/RNA/DNA / RNA polymerase II / initiation complex / TRANSCRIPTION-RNA-DNA HYBRID complex / TRANSCRIPTION-RNA-DNA complex
Function / homology
Function and homology information


RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / termination of RNA polymerase II transcription / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape ...RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / termination of RNA polymerase II transcription / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / Formation of TC-NER Pre-Incision Complex / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / termination of RNA polymerase I transcription / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / transcription by RNA polymerase III / Dual incision in TC-NER / translesion synthesis / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / transcription-coupled nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / ribonucleoside binding / DNA-directed RNA polymerase / cytoplasmic stress granule / DNA-directed RNA polymerase activity / peroxisome / ribosome biogenesis / nucleic acid binding / transcription by RNA polymerase II / protein dimerization activity / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / DCoH-like / RNA polymerase alpha subunit dimerisation domain / Hypothetical Protein Ta0175; Chain: A, domain 2 / Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L / Gyrase A; domain 2 - #140 / RPB5-like RNA polymerase subunit / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 ...Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / DCoH-like / RNA polymerase alpha subunit dimerisation domain / Hypothetical Protein Ta0175; Chain: A, domain 2 / Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L / Gyrase A; domain 2 - #140 / RPB5-like RNA polymerase subunit / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / N-terminal domain of TfIIb - #10 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / RNA polymerase II, Rpb2 subunit, wall domain / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase, RBP11-like subunit / Enzyme I; Chain A, domain 2 / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / DNA-directed RNA polymerase, insert domain / RNA Polymerase Alpha Subunit; Chain A, domain 2 / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / Gyrase A; domain 2 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Homeodomain-like / Zinc finger TFIIS-type signature. / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Single Sheet / Nucleic acid-binding proteins / Beta Complex / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / 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 / DNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / 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 RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsLiu, X. / Bushnell, D.A. / Silva, D.A. / Huang, X. / Kornberg, R.D.
CitationJournal: Science / Year: 2011
Title: Initiation complex structure and promoter proofreading.
Authors: Liu, X. / Bushnell, D.A. / Silva, D.A. / Huang, X. / Kornberg, R.D.
History
DepositionMay 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
A: DNA-directed RNA polymerase II subunit RPB1
B: DNA-directed RNA polymerase II subunit RPB2
C: DNA-directed RNA polymerase II subunit RPB3
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
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
R: RNA (5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*G)-3')
T: DNA (5'-D(*CP*TP*AP*CP*CP*GP*AP*TP*AP*AP*GP*CP*AP*GP*AP*CP*GP*AP*TP*CP*CP*TP*CP*TP*CP*GP*AP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)481,97221
Polymers481,42512
Non-polymers5489
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60930 Å2
ΔGint-307 kcal/mol
Surface area139990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.965, 220.896, 192.030
Angle α, β, γ (deg.)90.000, 98.160, 90.000
Int Tables number5
Space group name H-MC121

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Components

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DNA-directed RNA polymerase II subunit ... , 5 types, 5 molecules ABCIK

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


Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: CB010 / References: UniProt: P04050, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase II subunit RPB2 / RNA polymerase II subunit 2 / B150 / DNA-directed RNA polymerase II 140 kDa polypeptide


Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: CB010 / References: UniProt: P08518, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase II subunit RPB3 / RNA polymerase II subunit 3 / RNA polymerase II subunit B3 / B44.5 / DNA-directed RNA polymerase II ...RNA polymerase II subunit 3 / RNA polymerase II subunit B3 / B44.5 / DNA-directed RNA polymerase II 45 kDa polypeptide


Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: CB010 / References: UniProt: P16370
#7: Protein DNA-directed RNA polymerase II subunit RPB9 / 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: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: CB010 / References: UniProt: P27999
#9: Protein DNA-directed RNA polymerase II subunit RPB11 / RNA polymerase II subunit B11 / B13.6 / DNA-directed RNA polymerase II 13.6 kDa polypeptide


Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: CB010 / References: UniProt: P38902

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

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


Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: CB010 / References: UniProt: P20434
#5: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / II / and ...RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / II / and III 23 kDa polypeptide


Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: CB010 / References: UniProt: P20435
#6: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3 / 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 / II / and III 14.5 kDa polypeptide


Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: CB010 / References: UniProt: P20436
#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5 / 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 / II / and III 8.3 kDa polypeptide


Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: CB010 / References: UniProt: P22139
#10: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha


Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: CB010 / References: UniProt: P40422

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RNA chain / DNA chain , 2 types, 2 molecules RT

#11: RNA chain RNA (5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*G)-3')


Mass: 2934.831 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA (9-nt)
#12: DNA chain DNA (5'-D(*CP*TP*AP*CP*CP*GP*AP*TP*AP*AP*GP*CP*AP*GP*AP*CP*GP*AP*TP*CP*CP*TP*CP*TP*CP*GP*AP*TP*G)-3')


Mass: 8863.724 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Template DNA

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Non-polymers , 2 types, 9 molecules

#13: Chemical
ChemComp-ZN / ZINC ION


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


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

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Details

Compound detailsAN ADDITIONAL DNA CHAIN (14-NT) IN THE CRYSTA BUT THE WHOLE CHAIN IS DISORDERED AND THUS NOT ...AN ADDITIONAL DNA CHAIN (14-NT) IN THE CRYSTA BUT THE WHOLE CHAIN IS DISORDERED AND THUS NOT PRESENT IN THE MODEL: GATGGCTATTCGTC

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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: 3.49 Å3/Da / Density % sol: 64.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 390mM (NH4)2HPO4/NaH2PO4, pH 6.9, 50mM dioxane, 9-11% PEG 6,000, 15mM DTT, vapor diffusion, temperature 293K, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 109833 / % possible obs: 100 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.124 / Χ2: 1.202 / Net I/σ(I): 6.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.2-3.313.80.691109530.9831100
3.31-3.453.80.518109451.0081100
3.45-3.63.90.391109751.0581100
3.6-3.793.90.278109441.0981100
3.79-4.033.90.206110031.1551100
4.03-4.343.90.134109081.1881100
4.34-4.783.90.1109801.2521100
4.78-5.473.90.1110091.3281100
5.47-6.893.90.088110231.3021100
6.89-503.80.043110931.639199.7

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.8.0refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.1data extraction
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→43.65 Å / Cor.coef. Fo:Fc: 0.9059 / Cor.coef. Fo:Fc free: 0.8706 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2365 5511 5.02 %RANDOM
Rwork0.1884 ---
obs0.1908 109831 --
Displacement parametersBiso max: 247.6 Å2 / Biso mean: 103.836 Å2 / Biso min: 33 Å2
Baniso -1Baniso -2Baniso -3
1--36.8943 Å20 Å225.3566 Å2
2--15.2219 Å20 Å2
3---21.6724 Å2
Refine analyzeLuzzati coordinate error obs: 0.711 Å
Refinement stepCycle: LAST / Resolution: 3.2→43.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28292 456 9 0 28757
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d10632SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes767HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4139HARMONIC5
X-RAY DIFFRACTIONt_it29322HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion3871SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance32HARMONIC1
X-RAY DIFFRACTIONt_utility_angle45HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact34601SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d29322HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg39691HARMONIC21.26
X-RAY DIFFRACTIONt_omega_torsion2.66
X-RAY DIFFRACTIONt_other_torsion23.52
LS refinement shellResolution: 3.17→3.25 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3036 330 5.04 %
Rwork0.2516 6214 -
all0.2541 6544 -
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)
10.9330.65460.24831.56660.48161.31080.03370.32990.16140.0854-0.0302-0.4144-0.21660.5971-0.0035-0.0295-0.1196-0.10570.0450.1364-0.170849.4176-32.760435.9105
20.6155-0.36270.77970.7867-0.76171.5714-0.0079-0.05050.03120.16040.0914-0.21110.30540.4714-0.08350.1440.1397-0.0877-0.304-0.0663-0.338331.0862-63.637667.923
30.4365-0.00540.20370.81570.29611.24170.09540.01510.00860.0216-0.03020.030.0486-0.1808-0.06520.0202-0.11450.0111-0.3040.0917-0.3038-7.5381-35.430944.3472
4-0.03580.44170.68733.26280.17642.5931-0.10590.1910.09980.43020.2218-0.46860.04430.2524-0.11590.3222-0.1237-0.0692-0.304-0.1713-0.286829.9065-8.928190.345
50.007-0.0351-0.02650-0.00510.03120.0005-0.0003-0.00580.00060.0002-0.0030.0021-0.0001-0.00060.0123-0.01390.0030.02170.027-0.035824.1769-24.157127.4774
60.0220.0113-0.04250.0089-0.05160.0463-0.0010.00090.00030.00080.0005-0.00130.00290.00220.00050.0196-0.00710.00290.03350.0043-0.001724.5923-23.100231.5479
70.01380.0251-0.05030.011-0.06770.0298-0.0003-0.00230.00010-0.00210.00010.00060.00330.00240.0212-0.02480.00750.01210.0324-0.002523.3576-20.74935.7383
80.01460.0798-0.05230.0494-0.10430.02130.00070.0015-0.00120.0046-0.0004-0.00310.00160.0044-0.00030.0307-0.0167-0.0014-0.00650.02770.000818.8901-20.519238.2326
90.00910.0177-0.03170.1016-0.08310.007600.0010.00160.01020.0034-0.0047-0.00220.004-0.00340.0518-0.0157-0.0275-0.046-0.0186-0.017614.3912-21.093740.131
100.00230.0584-0.01130.0618-0.24270.0476-0.00060.0028-0.00090.0077-0.00120.0002-0.0022-0.00140.00180.0485-0.0283-0.0162-0.0370.0446-0.035610.2379-23.717640.9319
110.1540.08010.09610-0.08170.065-0.0023-0.01420.01960.0076-0.002-0.0026-0.01300.00440.0366-0.0464-0.0136-0.0125-0.0387-0.04178.1599-27.906341.6214
120.0025-0.2313-0.01240-0.20250.0507-0.003-0.00610.0038-0.0044-0.0107-0.005-0.003-0.00080.01370.0495-0.0194-0.046-0.00980.0685-0.07997.4143-33.363741.9563
130.0357-0.1206-0.12710.001-0.29450.08010.00020.00010.00020.00320.0008-0.0003-0.0001-0.008-0.0010.01550.0060.07510.02660.0943-0.04937.6355-37.602344.2748
140.0073-0.00190.0020.0256-0.00750.0083-0.00020.00060.000300.0005-0.000200.001-0.00020.0178-0.0156-0.00320.00330.00040.011635.4462-29.690952.8846
150.009500.00150.01520.00320.00020.0001-0.00160.00090.0033-0.00060.0031-0.0007-0.00010.00050.0109-0.0033-0.01030.00720.01290.00630.9998-32.33752.9503
160.00820.0081-0.02540.0444-0.09690.050.0006-0.00160.0021-0.0016-0.00030.0004-0.00110.0011-0.00030.03540.00670.0022-0.00020.0070.016525.947-31.53852.0149
170.0305-0.0336-0.0490.04360.02510.04390.0006-0.0030.00170.00060.0034-0.0062-0.0042-0.0026-0.0040.02970.0120.0198-0.0172-0.01470.020219.0459-35.844748.857
18-0.0058-0.02630.01910-0.07670.01610.0007-0.0021-0.0027-0.0013-0.0019-0.0032-0.004-0.00310.00110.0181-0.0353-0.015-0.06260.054-0.110618.409-38.033944.318
190.0324-0.0311-0.11070.0005-0.0743-0.03240.00090.0034-0.0047-0.00460.0015-0.0033-0.0001-0.0005-0.00240.0203-0.06050.0353-0.06070.0913-0.073416.8558-38.044340.1626
20-0.006-0.03520.01980-0.08550.01420.00070.0036-0.0057-0.00040.0020.00080.00570.0007-0.00260.036-0.022-0.0385-0.03380.0313-0.053314.1908-35.693736.8481
210.02040.0418-0.06970.006-0.0437-0.02040.00030.00490.0002-0.0053-0.00290.0079-0.004-0.00520.00260.022-0.04080.0125-0.04970.1228-0.080711.3217-32.148734.2472
220.00030.1342-0.00160-0.12540.0085-0.0001-0.00190.0011-0.006-0.00560.00490.0045-0.00250.00570.0267-0.05740.0754-0.04840.087-0.018610.3181-27.921832.49
23-0.0271-0.00170.09260-0.09380.02710.00150.0041-0.0001-0.0077-0.0030.0052-0.0043-0.00230.00150.0326-0.0207-0.0127-0.0370.0457-0.018410.3047-23.017131.4936
240.0078-0.0107-0.02660.0856-0.1318-0.0078-0.00110.0003-0.0023-0.0119-0.00090.01410.0014-0.0010.0020.0385-0.0843-0.0202-0.02190.031-0.026612.9181-18.348931.485
250.00590.0383-0.02250.04540.01830.0284-0.00090.00130.0048-0.004200.0061-0.0032-0.00080.00080.0327-0.0369-0.00930.00810.0308-0.00216.5003-15.162231.0513
260.02820.04010.01690.0277-0.03110.0495-0.00060.00050.0026-0.00160.00230.00170.0016-0.0016-0.00170.0337-0.0205-0.03690.0266-0.0010.011520.0917-13.069329.8833
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|3 - A|346 A|1395 - A|1445 B|1151 - B|1224 }A3 - 346
2X-RAY DIFFRACTION1{ A|3 - A|346 A|1395 - A|1445 B|1151 - B|1224 }A1395 - 1445
3X-RAY DIFFRACTION1{ A|3 - A|346 A|1395 - A|1445 B|1151 - B|1224 }B1151 - 1224
4X-RAY DIFFRACTION2{ A|809 - A|1141 A|1275 - A|1394 E|2 - E|215 F|72 - F|155 }A809 - 1141
5X-RAY DIFFRACTION2{ A|809 - A|1141 A|1275 - A|1394 E|2 - E|215 F|72 - F|155 }A1275 - 1394
6X-RAY DIFFRACTION2{ A|809 - A|1141 A|1275 - A|1394 E|2 - E|215 F|72 - F|155 }E2 - 215
7X-RAY DIFFRACTION2{ A|809 - A|1141 A|1275 - A|1394 E|2 - E|215 F|72 - F|155 }F72 - 155
8X-RAY DIFFRACTION3{ A|347 - A|808 B|20 - B|217 C|3 - C|268 B|406 - B|1150 J|1 - J|101 K|1 - K|114 L|25 - L|105 H|2 - H|146 I|40 - I|120 }A347 - 808
9X-RAY DIFFRACTION3{ A|347 - A|808 B|20 - B|217 C|3 - C|268 B|406 - B|1150 J|1 - J|101 K|1 - K|114 L|25 - L|105 H|2 - H|146 I|40 - I|120 }B20 - 217
10X-RAY DIFFRACTION3{ A|347 - A|808 B|20 - B|217 C|3 - C|268 B|406 - B|1150 J|1 - J|101 K|1 - K|114 L|25 - L|105 H|2 - H|146 I|40 - I|120 }C3 - 268
11X-RAY DIFFRACTION3{ A|347 - A|808 B|20 - B|217 C|3 - C|268 B|406 - B|1150 J|1 - J|101 K|1 - K|114 L|25 - L|105 H|2 - H|146 I|40 - I|120 }B406 - 1150
12X-RAY DIFFRACTION3{ A|347 - A|808 B|20 - B|217 C|3 - C|268 B|406 - B|1150 J|1 - J|101 K|1 - K|114 L|25 - L|105 H|2 - H|146 I|40 - I|120 }J1 - 101
13X-RAY DIFFRACTION3{ A|347 - A|808 B|20 - B|217 C|3 - C|268 B|406 - B|1150 J|1 - J|101 K|1 - K|114 L|25 - L|105 H|2 - H|146 I|40 - I|120 }K1 - 114
14X-RAY DIFFRACTION3{ A|347 - A|808 B|20 - B|217 C|3 - C|268 B|406 - B|1150 J|1 - J|101 K|1 - K|114 L|25 - L|105 H|2 - H|146 I|40 - I|120 }L25 - 105
15X-RAY DIFFRACTION3{ A|347 - A|808 B|20 - B|217 C|3 - C|268 B|406 - B|1150 J|1 - J|101 K|1 - K|114 L|25 - L|105 H|2 - H|146 I|40 - I|120 }H2 - 146
16X-RAY DIFFRACTION3{ A|347 - A|808 B|20 - B|217 C|3 - C|268 B|406 - B|1150 J|1 - J|101 K|1 - K|114 L|25 - L|105 H|2 - H|146 I|40 - I|120 }I40 - 120
17X-RAY DIFFRACTION4{ A|1142 - A|1272 B|218 - B|405 I|2 - I|39 }A1142 - 1272
18X-RAY DIFFRACTION4{ A|1142 - A|1272 B|218 - B|405 I|2 - I|39 }B218 - 405
19X-RAY DIFFRACTION4{ A|1142 - A|1272 B|218 - B|405 I|2 - I|39 }I2 - 39
20X-RAY DIFFRACTION5{ R|2 }R2
21X-RAY DIFFRACTION6{ R|3 }R3
22X-RAY DIFFRACTION7{ R|4 }R4
23X-RAY DIFFRACTION8{ R|5 }R5
24X-RAY DIFFRACTION9{ R|6 }R6
25X-RAY DIFFRACTION10{ R|7 }R7
26X-RAY DIFFRACTION11{ R|8 }R8
27X-RAY DIFFRACTION12{ R|9 }R9
28X-RAY DIFFRACTION13{ R|10 }R10
29X-RAY DIFFRACTION14{ T|16 }T16
30X-RAY DIFFRACTION15{ T|17 }T17
31X-RAY DIFFRACTION16{ T|18 }T18
32X-RAY DIFFRACTION17{ T|19 }T19
33X-RAY DIFFRACTION18{ T|20 }T20
34X-RAY DIFFRACTION19{ T|21 }T21
35X-RAY DIFFRACTION20{ T|22 }T22
36X-RAY DIFFRACTION21{ T|23 }T23
37X-RAY DIFFRACTION22{ T|24 }T24
38X-RAY DIFFRACTION23{ T|25 }T25
39X-RAY DIFFRACTION24{ T|26 }T26
40X-RAY DIFFRACTION25{ T|27 }T27
41X-RAY DIFFRACTION26{ T|28 }T28

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