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- PDB-3gto: Backtracked RNA polymerase II complex with 15mer RNA -

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Basic information

Entry
Database: PDB / ID: 3gto
TitleBacktracked RNA polymerase II complex with 15mer RNA
Components
  • (DNA-directed RNA polymerase II subunit ...) x 5
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • DNA (28-MER)
  • DNA (5'-D(*CP*TP*GP*CP*TP*TP*AP*TP*CP*GP*GP*TP*AP*G)-3')
  • RNA (5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*AP*UP*GP*CP*AP*C)-3')
KeywordsTRANSCRIPTION / TRANSFERASE/DNA-RNA HYBRID / TRANSFERASE / DNA-RNA HYBRID / Backtrack / DNA-directed RNA polymerase / DNA binding / Isopeptide bond / Magnesium / Metal binding / Nucleotidyltransferase / Nucleus / Phosphoprotein / Zinc-finger / DNA damage / DNA repair / TRANSFERASE-DNA-RNA HYBRID 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 / transcription initiation at RNA polymerase I promoter / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / 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
RNA polymerase ii / 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 ...RNA polymerase ii / 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 / Barwin-like endoglucanases - #20 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / RNA polymerase II, Rpb2 subunit, wall domain / Barwin-like endoglucanases / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain / RNA polymerase, RBP11-like subunit / Enzyme I; Chain A, domain 2 / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / Topoisomerase I; Chain A, domain 4 / 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. / Gyrase A; domain 2 / 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 / 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 / Dna Ligase; domain 1 / 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
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / 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 / DNA (> 10) / RNA / RNA (> 10) / 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: 4 Å
AuthorsWang, D. / Bushnell, D.A. / Huang, X. / Westover, K.D. / Levitt, M. / Kornberg, R.D.
CitationJournal: Science / Year: 2009
Title: Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution.
Authors: Wang, D. / Bushnell, D.A. / Huang, X. / Westover, K.D. / Levitt, M. / Kornberg, R.D.
History
DepositionMar 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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*GP*AP*UP*GP*CP*AP*C)-3')
T: DNA (28-MER)
N: DNA (5'-D(*CP*TP*GP*CP*TP*TP*AP*TP*CP*GP*GP*TP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)487,85022
Polymers487,30213
Non-polymers5489
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area65410 Å2
ΔGint-317.3 kcal/mol
Surface area148850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.851, 222.804, 194.977
Angle α, β, γ (deg.)90.00, 101.98, 90.00
Int Tables number5
Space group name H-MC121
DetailsASYMMETRIC UNIT IS THE BIOLOGICAL UNIT

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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 B1 / RNA polymerase II subunit 1 / DNA-directed RNA polymerase III ...RNA polymerase II subunit B1 / RNA polymerase II subunit 1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit B220


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


Mass: 138937.297 Da / Num. of mol.: 1
Fragment: DNA-directed RNA polymerase II 140 kDa polypeptide
Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P08518, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase II subunit RPB3 / RNA polymerase II subunit B3 / RNA polymerase II subunit 3 / DNA-directed RNA polymerase II 45 kDa ...RNA polymerase II subunit B3 / RNA polymerase II subunit 3 / DNA-directed RNA polymerase II 45 kDa polypeptide / B44.5


Mass: 35330.457 Da / Num. of mol.: 1 / Fragment: DNA-directed RNA polymerase II 45 kDa polypeptide / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P16370
#7: Protein DNA-directed RNA polymerase II subunit RPB9 / RNA polymerase II subunit B9 / DNA-directed RNA polymerase II subunit 9 / DNA-directed RNA ...RNA polymerase II subunit B9 / DNA-directed RNA polymerase II subunit 9 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / B12.6


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


Mass: 13633.493 Da / Num. of mol.: 1
Fragment: DNA-directed RNA polymerase II 13.6 kDa polypeptide
Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / 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 / DNA-directed RNA polymerases I / II / and III 27 ...RNA polymerases I / II / and III subunit ABC1 / DNA-directed RNA polymerases I / II / and III 27 kDa polypeptide / ABC27


Mass: 25117.094 Da / Num. of mol.: 1
Fragment: DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide
Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20434
#5: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerases I / II / and III 23 ...RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerases I / II / and III 23 kDa polypeptide / ABC23


Mass: 17931.834 Da / Num. of mol.: 1
Fragment: DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide
Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20435
#6: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerases I / II / and III subunit ABC3 / DNA-directed RNA polymerases I / II / and III 14.5 ...RNA polymerases I / II / and III subunit ABC3 / DNA-directed RNA polymerases I / II / and III 14.5 kDa polypeptide / ABC14.5 / ABC14.4


Mass: 16525.363 Da / Num. of mol.: 1
Fragment: DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide
Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20436
#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerases I / II / and III subunit ABC5 / DNA-directed RNA polymerases I / II / and III 8.3 ...RNA polymerases I / II / and III subunit ABC5 / DNA-directed RNA polymerases I / II / and III 8.3 kDa polypeptide / ABC10-beta / ABC8


Mass: 8290.732 Da / Num. of mol.: 1 / Fragment: DNA-directed RNA polymerases I/II/III subunit 10 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / 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
Fragment: DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide
Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40422

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RNA chain , 1 types, 1 molecules R

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


Mass: 4854.977 Da / Num. of mol.: 1 / Fragment: RNA strand / Source method: obtained synthetically / Details: Synthetic RNA

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DNA chain , 2 types, 2 molecules TN

#12: DNA chain DNA (28-MER)


Mass: 8534.519 Da / Num. of mol.: 1 / Fragment: DNA template strand / Source method: obtained synthetically / Details: Synthetic template DNA
#13: DNA chain DNA (5'-D(*CP*TP*GP*CP*TP*TP*AP*TP*CP*GP*GP*TP*AP*G)-3')


Mass: 4286.789 Da / Num. of mol.: 1 / Fragment: DNA non-template strand / Source method: obtained synthetically / Details: Synthetic non-template DNA

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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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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.72 Å3/Da / Density % sol: 66.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM Dioxane, 10mM DTT, 9-11% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2HPO4/NaH2PO411
2Dioxane11
3DTT11
4PEG 600011
5(NH4)2HPO4/NaH2PO412
6Dioxane12
7DTT12
8PEG 600012

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.211
SYNCHROTRONALS 5.0.221
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDNov 7, 2007
ADSC QUANTUM 3152CCDNov 7, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21
ReflectionResolution: 4→50 Å / Num. obs: 54082 / % possible obs: 90.4 % / Redundancy: 3.6 % / Net I/σ(I): 7.7
Reflection shellResolution: 4→4.1 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2 / % possible all: 77.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GTG

3gtg


Resolution: 4→50 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.874 / SU B: 135.474 / SU ML: 0.8 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.894 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28979 2847 5.1 %RANDOM
Rwork0.26865 ---
obs0.26973 53353 93.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 125.304 Å2
Baniso -1Baniso -2Baniso -3
1-6.61 Å20 Å2-8.71 Å2
2---7.93 Å20 Å2
3----2.3 Å2
Refinement stepCycle: LAST / Resolution: 4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28140 1110 9 0 29259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.02229910
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.792.01740623
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.80653518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.33424.0291333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.895155251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.45415222
X-RAY DIFFRACTIONr_chiral_restr0.120.24569
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0222007
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2790.214558
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.219193
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.21031
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3030.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2460.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7051.518262
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.066228569
X-RAY DIFFRACTIONr_scbond_it1.1313633
X-RAY DIFFRACTIONr_scangle_it1.7244.512054
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 4→4.11 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 182 -
Rwork0.352 3320 -
obs--79.55 %
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)
11.30330.86880.36341.082-0.00960.22740.120.01750.10380.0384-0.0007-0.11120.03140.1984-0.11920-0.0001-0.00010-0.0002047.4086.519339.4344
20.3789-0.24270.01990.4377-0.08950.49940.0524-0.05440.0530.12090.0409-0.02540.11350.1191-0.0933-0.02330.0165-0.1136-0.09420.0371-0.065127.0793-25.57869.7533
30.2030.02480.1430.34980.14710.28190.04310.00710.03090.0539-0.00820.01750.0348-0.0886-0.0349-0.1373-0.05810.044-0.05550.0494-0.0425-10.6763.343944.1721
40.06470.10220.24720.8536-0.01621.1838-0.13510.0483-0.01990.36430.153-0.2204-0.16940.0008-0.017900.0001000.0001024.587629.478292.2894
50.2269-0.40340.2620.7178-0.44781.1288-0.12020.13690.2525-0.0704-0.10210.00080.14640.5880.22230.000100.0001-0.0001-0.0001-0.000131.14611.481360.0005
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 154
2X-RAY DIFFRACTION1A161 - 186
3X-RAY DIFFRACTION1A199 - 346
4X-RAY DIFFRACTION1A1395 - 1445
5X-RAY DIFFRACTION1B1151 - 1224
6X-RAY DIFFRACTION2A809 - 1141
7X-RAY DIFFRACTION2A1275 - 1394
8X-RAY DIFFRACTION2E2 - 215
9X-RAY DIFFRACTION2F72 - 155
10X-RAY DIFFRACTION3A347 - 808
11X-RAY DIFFRACTION3B20 - 70
12X-RAY DIFFRACTION3B90 - 217
13X-RAY DIFFRACTION3C3 - 268
14X-RAY DIFFRACTION3B406 - 437
15X-RAY DIFFRACTION3B446 - 668
16X-RAY DIFFRACTION3B678 - 715
17X-RAY DIFFRACTION3B722 - 919
18X-RAY DIFFRACTION3B933 - 1150
19X-RAY DIFFRACTION3J1 - 65
20X-RAY DIFFRACTION3K1 - 114
21X-RAY DIFFRACTION3L25 - 70
22X-RAY DIFFRACTION3H2 - 63
23X-RAY DIFFRACTION3H76 - 146
24X-RAY DIFFRACTION3I40 - 120
25X-RAY DIFFRACTION4A1142 - 1176
26X-RAY DIFFRACTION4A1187 - 1272
27X-RAY DIFFRACTION4B218 - 335
28X-RAY DIFFRACTION4B345 - 405
29X-RAY DIFFRACTION4I2 - 39
30X-RAY DIFFRACTION5N1 - 14
31X-RAY DIFFRACTION5T1 - 28
32X-RAY DIFFRACTION5R1 - 12

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