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- PDB-3s16: RNA Polymerase II Initiation Complex with an 8-nt RNA -

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Basic information

Entry
Database: PDB / ID: 3s16
TitleRNA Polymerase II Initiation Complex with an 8-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(*UP*CP*GP*AP*GP*AP*GP*G)-3')
KeywordsTRANSCRIPTION/RNA/DNA / RNA polymerase II / initiation 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 / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase III promoter / termination of RNA polymerase I transcription / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / Estrogen-dependent gene expression / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Dual incision in TC-NER / transcription by RNA polymerase III / transcription by RNA polymerase I / translesion synthesis / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / : / DNA-directed RNA polymerase activity / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / cytoplasmic stress granule / peroxisome / ribosome biogenesis / transcription by RNA polymerase II / nucleic acid binding / 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 / 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 / Gyrase A; domain 2 / 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. / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / 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: 3.241 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 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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(*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)481,64321
Polymers481,09512
Non-polymers5489
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60430 Å2
ΔGint-312 kcal/mol
Surface area142440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.843, 221.125, 192.746
Angle α, β, γ (deg.)90.000, 97.610, 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(*UP*CP*GP*AP*GP*AP*GP*G)-3')


Mass: 2605.625 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA (8-mer)
#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 CRYSTAL BUT THE WHOLE CHAIN IS DISORDERED AND THUS NOT ...AN ADDITIONAL DNA CHAIN (14-NT) IN THE CRYSTAL 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: 3.47 Å3/Da / Density % sol: 64.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM dioxane, 9-11% PEG 6.000, 15mM DTT, vapor diffusion, temperature 293K

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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 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.241→29.865 Å / Num. all: 103014 / Num. obs: 103014 / % possible obs: 99.4 % / Redundancy: 3.9 % / Rsym value: 0.146 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.24-3.423.80.811155439145690.81196.6
3.42-3.623.90.5261.555366142890.526100
3.62-3.873.90.3332.352283134790.333100
3.87-4.183.90.213.548391124760.21100
4.18-4.583.90.1395.244734115200.139100
4.58-5.123.90.1146.440362104030.114100
5.12-5.923.90.1146.53585592350.114100
5.92-7.253.90.0927.83017577830.092100
7.25-10.253.90.0659.82334660420.065100
10.25-29.8653.80.05212.51224832180.05295.9

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.8.0refinement
SCALA3.3.16data processing
PDB_EXTRACT3.1data extraction
SCALAdata scaling
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NVQ

2nvq


Resolution: 3.241→29.865 Å / Cor.coef. Fo:Fc: 0.9156 / Cor.coef. Fo:Fc free: 0.8811 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2271 5152 5 %RANDOM
Rwork0.1833 ---
obs0.1855 102993 --
Displacement parametersBiso max: 300 Å2 / Biso mean: 113.1299 Å2 / Biso min: 12.27 Å2
Baniso -1Baniso -2Baniso -3
1--23.9139 Å20 Å218.201 Å2
2---1.5987 Å20 Å2
3---25.5126 Å2
Refine analyzeLuzzati coordinate error obs: 0.713 Å
Refinement stepCycle: LAST / Resolution: 3.241→29.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28292 434 9 0 28735
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d10620SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes767HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4138HARMONIC5
X-RAY DIFFRACTIONt_it29297HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion3867SEMIHARMONIC5
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_contact33434SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d29297HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg39652HARMONIC21.18
X-RAY DIFFRACTIONt_omega_torsion2.31
X-RAY DIFFRACTIONt_other_torsion23.31
LS refinement shellResolution: 3.24→3.32 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3176 392 5.59 %
Rwork0.2598 6618 -
all0.2631 7010 -
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)
10.87450.18890.15171.4030.35140.70520.05290.23050.16510.0005-0.0402-0.3009-0.10.5495-0.01270.097-0.1705-0.10240.27780.1299-0.308250.0084-33.369535.4056
20.7103-0.29760.75890.7403-0.58281.84140.0182-0.1211-0.00270.09970.1231-0.06730.32270.5329-0.14130.0170.1451-0.1091-0.1274-0.0482-0.338831.3439-64.183768.0171
30.41110.02410.27170.89920.33161.81920.06880.01780.0064-0.0988-0.05950.0948-0.1398-0.2114-0.0093-0.086-0.1056-0.0153-0.3040.0897-0.3119-7.2649-35.56244.5041
40.56941.01440.91713.03770.59573.0698-0.1320.15490.00230.28490.1599-0.3998-0.00910.3794-0.02790.3322-0.1305-0.067-0.304-0.1708-0.333230.8105-9.122690.4664
50.00750.0148-0.00780.0196-0.01490.010400.00030.00020.00090.00020.00120.00030.001-0.00020.0139-0.0091-0.01240.01210.01260.001324.6428-23.702731.6689
60.02060.0465-0.00490.01470.00720.0301-0.00010-0.00170.00130-0.00310.00250.0020.00010.0173-0.00960.00640.00820.00190.012123.8239-21.886436.1234
70-0.0115-0.00040.01650.02720.00750.0009-0.000100.0023-0.0001-0.0022-0.00110.0019-0.00080.0221-0.01-0.0195-0.0049-0.0104-0.012518.9648-20.930638.2447
80.0110.0341-0.01610.0003-0.07010.00230.00140.0027-0.00550.0018-0.00270.00180.00040.0030.00120.026-0.0128-0.0166-0.0157-0.0086-0.019314.9662-21.514140.4146
90.0190.0212-0.03380.092-0.14980.026-0.0014-0.0020.00130.00370.0008-0.00160.00060.00080.00060.035-0.0272-0.0435-0.00360.0093-0.01210.6611-24.177641.2484
100.13750.08550.00260-0.06030.0213-0.0017-0.01050.01390.0038-0.0029-0.0049-0.006-0.0040.00460.0198-0.0409-0.0053-0.0258-0.0397-0.01688.511-28.431941.852
110.003-0.1546-0.01130-0.1173-0.0021-0.0019-0.0040.0017-0.0037-0.0072-0.0104-0.0045-0.00060.00910.0442-0.025-0.0286-0.03940.0824-0.08657.8391-33.754642.1822
120.0055-0.0402-0.02630-0.14030.10390.00040.0014-0.00570.001-0.00150.00160.00360.00110.00110.01720.00960.01640.03570.0595-0.03438.2164-37.988544.2934
130.0030.0043-0.00390.0255-0.00770.009500.0015-0.00060.00130.0002-0.0010.00020.0015-0.00020.0152-0.0114-0.00540.0064-0.0020.009536.5309-30.325952.8808
140.0292-0.0030.03550.009-0.00960.0183-0.0003-0.00010.00130.00180.0002-0.00020.00060.00090.00010.00430.0025-0.01050.01560.00610.016230.996-32.861952.4971
150.0013-0.02620.00950.0337-0.05230.05150.0001-0.00120.0008-0.0026-0.00050.00230.0011-0.00130.00040.02270.0073-0.00880.0072-0.0070.011226.0034-32.049651.6678
160.00510.02230.0140.0047-0.02210.09020.00010.00110.0015-0.0010.0019-0.0101-0.00410.002-0.0020.03990.01530.02760.02320.0046-0.003819.2207-36.336648.7374
17-0.01110.0560.04070-0.13630.01110.0005-0.0004-0.0043-0.0006-0.00070.0017-0.0014-0.00050.00020.015-0.0111-0.0102-0.04050.0747-0.150919.0099-38.429544.4168
180.0134-0.0584-0.04920-0.0678-0.0132-0.00030.0001-0.0027-0.00460.0040-0.00120.0001-0.00370.0077-0.03310.017-0.06620.0806-0.086317.4049-38.444640.1833
19-0.007-0.07560.02440-0.03590.03310.0006-0.0040.00540.00390.00080.0036-0.00090.0007-0.00140.0179-0.0173-0.0327-0.0334-0.0174-0.046114.5669-35.987736.8415
200-0.04720.00010.0186-0.020200.00020.00360.001-0.0033-0.00170.0028-0.001-0.00060.00150.03420.0168-0.0206-0.00960.0449-0.025811.7409-32.460634.2085
21-0.00030.0518-0.00030.0228-0.03540.0237-0.0008-0.00420.0062-0.0045-0.0005-0.0010.0013-0.00040.00130.0312-0.03240.0226-0.02130.0364-0.002610.6569-28.198132.4763
22-0.03060.02940.11250.0001-0.04380.0306-0.0004-0.00470.0056-0.002600-0.00260.00130.00050.0215-0.0019-0.0278-0.0430.0329-0.027610.5857-23.094131.4897
23-0.00330.05170.0120-0.2390.0033-0.001-0.00050.0019-0.00340.00360.00360.00230.0035-0.00260.0258-0.06070.0154-0.02660.0684-0.025213.1203-18.33531.7109
240.02330.0474-0.0140.02660.0003-0.0041-0.00050.00260.0001-0.00220.00210.00040.00120.0032-0.00160.0083-0.0401-0.0090.0010.00260.005117.005-15.52230.9984
250.03810.0226-0.00420.0345-0.0450.052500.00060.00350.00060.00180.002-0.0014-0.0025-0.00180.029-0.0111-0.00120.02370.01170.024920.5673-13.326828.7308
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|3 }R3
21X-RAY DIFFRACTION6{ R|4 }R4
22X-RAY DIFFRACTION7{ R|5 }R5
23X-RAY DIFFRACTION8{ R|6 }R6
24X-RAY DIFFRACTION9{ R|7 }R7
25X-RAY DIFFRACTION10{ R|8 }R8
26X-RAY DIFFRACTION11{ R|9 }R9
27X-RAY DIFFRACTION12{ R|10 }R10
28X-RAY DIFFRACTION13{ T|16 }T16
29X-RAY DIFFRACTION14{ T|17 }T17
30X-RAY DIFFRACTION15{ T|18 }T18
31X-RAY DIFFRACTION16{ T|19 }T19
32X-RAY DIFFRACTION17{ T|20 }T20
33X-RAY DIFFRACTION18{ T|21 }T21
34X-RAY DIFFRACTION19{ T|22 }T22
35X-RAY DIFFRACTION20{ T|23 }T23
36X-RAY DIFFRACTION21{ T|24 }T24
37X-RAY DIFFRACTION22{ T|25 }T25
38X-RAY DIFFRACTION23{ T|26 }T26
39X-RAY DIFFRACTION24{ T|27 }T27
40X-RAY DIFFRACTION25{ T|28 }T28

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