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- PDB-3s1q: RNA Polymerase II Initiation Complex with a 5-nt 3'-deoxy RNA soa... -

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Basic information

Entry
Database: PDB / ID: 3s1q
TitleRNA Polymerase II Initiation Complex with a 5-nt 3'-deoxy RNA soaked with ATP
Components
  • (DNA-directed RNA polymerase II subunit ...Polymerase) x 5
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) 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*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 / termination of RNA polymerase II transcription / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes ...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 / termination of RNA polymerase II transcription / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / Estrogen-dependent gene expression / 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 / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Dual incision in TC-NER / RNA polymerase I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / tRNA transcription by RNA polymerase III / 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 / transcription elongation by RNA polymerase I / RNA polymerase II activity / transcription-coupled nucleotide-excision repair / translesion synthesis / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / RNA polymerase II, core complex / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / peroxisome / cytoplasmic stress granule / 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 / RPB5-like RNA polymerase subunit / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 ...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 / RPB5-like RNA polymerase subunit / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase II, Rpb2 subunit, wall domain / N-terminal domain of TfIIb - #10 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / 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 / Zinc finger TFIIS-type signature. / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / 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 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 Rpo11 / 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 Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerases L / 13 to 16 Kd subunits signature. / Homeodomain-like / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / 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, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / 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 / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / 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 ...ADENOSINE-5'-TRIPHOSPHATE / 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: 3.3 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 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 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_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*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)481,21823
Polymers480,13912
Non-polymers1,07911
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area61750 Å2
ΔGint-316 kcal/mol
Surface area140040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.940, 220.530, 193.720
Angle α, β, γ (deg.)90.000, 98.480, 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 / Polymerase / 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 / Polymerase / 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 / Polymerase / 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 / 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: 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 / Polymerase / 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 polymerase / 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 polymerase / 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 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 / 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 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 / 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 polymerase / 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*GP*AP*GP*G)-3')


Mass: 1649.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 3'-deoxy RNA (5-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 , 3 types, 11 molecules

#13: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#14: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#15: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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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: 3.56 Å3/Da / Density % sol: 65.48 %
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, 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 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.3→29.666 Å / Num. obs: 100159 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 82.844 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 8.92
Reflection shell

Rmerge(I) obs: 0.01 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
3.3-3.381.626804713995.7
3.38-3.481.927873720599.9
3.48-3.582.427323707099.9
3.58-3.69326491686099.8
3.69-3.813.925733664499.8
3.81-3.944.524627637299.8
3.94-4.09623935619599.7
4.09-4.267.323072597599.6
4.26-4.459.421958569899.6
4.45-4.6710.421016546399.6
4.67-4.9211.619918519299.8
4.92-5.2211.718874492499.6
5.22-5.5811.917664460899.6
5.58-6.0212.816635433099.5
6.02-6.614.214933392299.5
6.6-7.3817.413658360899.4
7.38-8.5223.311989317499.4
8.52-10.4327.49951267999.5
10.43-14.7529.47682208999.5
14.7529.73601101286.3

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.8.0refinement
XSCALEdata processing
PDB_EXTRACT3.1data extraction
XSCALEdata scaling
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→29.666 Å / Cor.coef. Fo:Fc: 0.8951 / Cor.coef. Fo:Fc free: 0.8641 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.229 4995 5 %RANDOM
Rwork0.1758 ---
obs0.1785 99954 --
Displacement parametersBiso max: 300 Å2 / Biso mean: 136.9312 Å2 / Biso min: 52.95 Å2
Baniso -1Baniso -2Baniso -3
1--51.7396 Å20 Å247.8457 Å2
2--21.3447 Å20 Å2
3---30.3949 Å2
Refine analyzeLuzzati coordinate error obs: 0.849 Å
Refinement stepCycle: LAST / Resolution: 3.3→29.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28292 370 41 0 28703
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d10601SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes771HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4137HARMONIC5
X-RAY DIFFRACTIONt_it29259HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion4HARMONIC0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion3854SEMIHARMONIC5
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_contact34690SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d29259HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg39593HARMONIC21.36
X-RAY DIFFRACTIONt_omega_torsion2.75
X-RAY DIFFRACTIONt_other_torsion24.54
LS refinement shellResolution: 3.3→3.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 349 4.98 %
Rwork0.2609 6666 -
all0.2617 7015 -
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)
10.41450.3156-0.04450.66640.06890.8438-0.02250.25910.27650.04220.0041-0.3111-0.07230.58610.0184-0.2711-0.0868-0.11850.23870.14070.199449.1297-32.62236.3621
20.7021-0.41870.46670.6382-0.43071.36930.0696-0.06880.01750.08160.1088-0.09670.42620.3392-0.17840.10430.1136-0.1286-0.1355-0.0102-0.094131.0813-63.784668.2142
30.5076-0.14010.27990.57560.14231.11450.10740.0108-0.03050.059-0.03530.06580.1499-0.1829-0.0721-0.1818-0.130.0994-0.17330.0887-0.1941-7.7965-35.99644.5905
40.9835-0.1880.89882.1995-0.40612.6258-0.1590.10910.11970.530.2241-0.4525-0.0530.2559-0.06510.1836-0.072-0.0946-0.2422-0.1641-0.036529.3888-9.168791.0341
50.0097-0.05890.00690.0003-0.01950.00180.0010.0039-0.0036-0.0035-0.00090.00170.00330.0031-0.00020.01660.0152-0.00330.0015-0.0194-0.012114.5869-22.312240.7537
60.2141-0.07690.00620.0855-0.12620.0327-0.0012-0.00150.00310.00660.002-0.0078-0.00260.0053-0.00080.04160.0107-0.02740.02-0.01270.023110.2588-24.420641.3309
70.1740.14350.048200.05440.0293-0.001-0.01140.00830.00360.0008-0.0074-0.0019-0.00610.00020.0081-0.0411-0.0119-0.0022-0.07290.018.0538-28.453742.0958
8-0.0214-0.17390.06950-0.08470.0288-0.0005-0.0042-0.0026-0.0017-0.0078-0.0205-0.00730.00970.00830.0354-0.0089-0.054-0.03770.005-0.07537.0421-33.901442.4097
90.0006-0.0167-0.01750-0.14040.20680.00110.00130.0010.0052-0.00130.023-0.011-0.00040.00010.05420.0273-0.0560.03580.0547-0.08086.9924-37.73944.6314
100.041-0.06450.00810.0965-0.04950.031400.00560.0043-0.0003-0.0008-0.0015-0.0008-0.00150.00080.0251-0.03080.00680.01320.01490.03736.3578-28.860853.7893
110.0098-0.0423-0.021500.0195-0.0066-0.0008-0.00620.00670.0103-0.00050.0042-0.00620.00120.00130.0088-0.0074-0.0170.00740.02240.005131.2411-30.777952.7433
120.0178-0.0139-0.06020-0.05550.00660.0005-0.01130.00760.0024-0.00220.0014-0.00590.00330.00170.0180.01570.0097-0.02330.06320.005726.0829-31.146752.3743
130.0126-0.0168-0.04120.0373-0.0127-0.0125-0.0007-0.00740.0076-0.00350.007-0.0088-0.0031-0.0039-0.00620.0239-0.036-0.01-0.07180.0225-0.022619.1762-36.356249.6514
140.00840.017-0.03050.0022-0.07940.03120.00030.0016-0.00070.00280.0017-0.008-0.00610.0052-0.00190.0289-0.07490.00380.00910.0326-0.026318.1186-38.510744.8663
150.0170.0135-0.05580-0.11570.0154-0.00120.00330.0027-0.00150.0003-0.0050.0021-0.00170.00090.0162-0.01370.0019-0.01270.0866-0.028416.6375-38.304240.4827
160.0024-0.1372-0.00790-0.0382-0.00240.0004-0.00530.00620.001-0.00240.0011-0.00160.00540.002-0.00940.0027-0.0197-0.02840.0392-0.030713.9258-36.106337.119
170.00570.0053-0.01870.0207-0.0764-0.0057-0.00020.00760.0009-0.004-0.00410.0021-0.00010.00060.00430.0204-0.0265-0.004-0.04380.0848-0.044411.2561-32.806134.4534
180.0060.0828-0.02060-0.10040.00730.00020.0032-0.0037-0.0086-0.00510.0070.0003-0.00350.00490.0244-0.02450.0141-0.00770.0728-0.02119.9327-28.306532.8376
19-0.00450.09030.014800.00220.0045-0.0012-0.00040.00930.00140.003-0.0032-0.0023-0.0017-0.00180.0023-0.003-0.0092-0.01570.0348-0.002110.1975-23.052731.8849
200.06260.0339-0.00880.0377-0.05880.0277-0.00050.00490.0022-0.00220.00290.0029-0.00050.0044-0.00240.02710.0006-0.0221-0.0120.03760.046611.91-20.133929.7884
210.04240.0196-0.01190.04080.00740.0464-0.00030.00220.0032-0.00120.00030.0035-0.0026-0.0023-0.00010.0227-0.02040.00190.0213-0.01110.025716.127-15.869831.9284
220.04180.03370.01370.0406-0.03610.0753-0.0006-0.00110.00250.00060.00120.00230.0008-0.0057-0.00060.0324-0.0067-0.02040.0434-0.00130.029420.8144-13.485730.763
23-0.0309-0.01290.22510.0299-0.08360.19210.0005-0.0016-0.00770.0089-0.00160.0332-0.0009-0.02020.00110.0265-0.0468-0.02920.014-0.009-0.05016.7082-40.508349.1871
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|6 }R6
21X-RAY DIFFRACTION6{ R|7 }R7
22X-RAY DIFFRACTION7{ R|8 }R8
23X-RAY DIFFRACTION8{ R|9 }R9
24X-RAY DIFFRACTION9{ R|10 }R10
25X-RAY DIFFRACTION10{ T|16 }T16
26X-RAY DIFFRACTION11{ T|17 }T17
27X-RAY DIFFRACTION12{ T|18 }T18
28X-RAY DIFFRACTION13{ T|19 }T19
29X-RAY DIFFRACTION14{ T|20 }T20
30X-RAY DIFFRACTION15{ T|21 }T21
31X-RAY DIFFRACTION16{ T|22 }T22
32X-RAY DIFFRACTION17{ T|23 }T23
33X-RAY DIFFRACTION18{ T|24 }T24
34X-RAY DIFFRACTION19{ T|25 }T25
35X-RAY DIFFRACTION20{ T|26 }T26
36X-RAY DIFFRACTION21{ T|27 }T27
37X-RAY DIFFRACTION22{ T|28 }T28
38X-RAY DIFFRACTION23{ R|100 }0

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