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- PDB-6blo: Pol II elongation complex with an abasic lesion at i+1 position -

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Basic information

Entry
Database: PDB / ID: 6blo
TitlePol II elongation complex with an abasic lesion at i+1 position
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(P*AP*(3DR)P*CP*TP*CP*TP*CP*GP*AP*TP*G)-3')
  • RNA (5'-R(P*AP*UP*CP*GP*AP*GP*AP*G)-3')
KeywordsTRANSCRIPTION / Complex / DNA BINDING PROTEIN / DNA-RNA HYBRID
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
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 / 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 ...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 / 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 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 / 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 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. / 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 / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / 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. / Homeodomain-like / 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 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / DNA-directed RNA polymerase, insert 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.401 Å
AuthorsWang, W. / Wang, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM102362 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II.
Authors: Wang, W. / Walmacq, C. / Chong, J. / Kashlev, M. / Wang, D.
History
DepositionNov 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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
T: DNA (5'-D(P*AP*(3DR)P*CP*TP*CP*TP*CP*GP*AP*TP*G)-3')
R: RNA (5'-R(P*AP*UP*CP*GP*AP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)481,54321
Polymers480,99512
Non-polymers5489
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60480 Å2
ΔGint-356 kcal/mol
Surface area136610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.550, 222.280, 193.770
Angle α, β, γ (deg.)90.00, 100.62, 90.00
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 B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II ...RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit B220


Mass: 191821.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPO21, RPB1, RPB220, SUA8, YDL140C, D2150 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04050, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase II subunit RPB2 / Polymerase / RNA polymerase II subunit 2 / B150 / DNA-directed RNA polymerase II 140 kDa polypeptide


Mass: 138937.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPB2, RPB150, RPO22, YOR151C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P08518, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase II subunit RPB3 / Polymerase / RNA polymerase II subunit B3 / B44.5 / DNA-directed RNA polymerase II 45 kDa polypeptide


Mass: 35330.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPB3, YIL021W / Production host: Saccharomyces cerevisiae (brewer's yeast) / 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 genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPB9, YGL070C / Production host: Saccharomyces cerevisiae (brewer's yeast) / 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 genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPB11, YOL005C / Production host: 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 polymerase / RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 ...RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 kDa polypeptide


Mass: 25117.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPB5, RPA7, RPC9, YBR154C, YBR1204 / Production host: Saccharomyces cerevisiae (brewer's yeast) / 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 / and III 23 ...RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 kDa polypeptide


Mass: 17931.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPO26, RPB6, YPR187W, P9677.8 / Production host: Saccharomyces cerevisiae (brewer's yeast) / 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 / and III 14.5 kDa polypeptide


Mass: 16525.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPB8, YOR224C, YOR50-14 / Production host: Saccharomyces cerevisiae (brewer's yeast) / 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 / and III 8.3 kDa polypeptide


Mass: 8290.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPB10, YOR210W / Production host: Saccharomyces cerevisiae (brewer's yeast) / 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 genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPC10, RPB12, YHR143W-A, YHR143BW / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40422

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

#11: DNA chain DNA (5'-D(P*AP*(3DR)P*CP*TP*CP*TP*CP*GP*AP*TP*G)-3')


Mass: 8779.650 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#12: RNA chain RNA (5'-R(P*AP*UP*CP*GP*AP*GP*AP*G)-3')


Mass: 2589.625 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.71 Å3/Da / Density % sol: 66.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 50mM dioxane, 10mM DTT, 9-12% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→63.5 Å / Num. obs: 83242 / % possible obs: 100 % / Redundancy: 3.7 % / Net I/σ(I): 5.2

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 3.401→63.484 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.58
RfactorNum. reflection% reflection
Rfree0.2272 4034 4.85 %
Rwork0.2025 --
obs0.2037 83193 86.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.401→63.484 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27808 389 9 0 28206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00228771
X-RAY DIFFRACTIONf_angle_d0.57538929
X-RAY DIFFRACTIONf_dihedral_angle_d11.92510971
X-RAY DIFFRACTIONf_chiral_restr0.0234377
X-RAY DIFFRACTIONf_plane_restr0.0024972
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4009-3.44090.2907230.3007573X-RAY DIFFRACTION18
3.4409-3.48290.3267500.29461044X-RAY DIFFRACTION33
3.4829-3.52690.2802840.29241355X-RAY DIFFRACTION44
3.5269-3.57340.2908740.27921655X-RAY DIFFRACTION52
3.5734-3.62230.27461030.2761825X-RAY DIFFRACTION59
3.6223-3.6740.32941090.26832125X-RAY DIFFRACTION67
3.674-3.72890.27651130.25922338X-RAY DIFFRACTION75
3.7289-3.78710.27771390.26062532X-RAY DIFFRACTION81
3.7871-3.84920.28321380.25752774X-RAY DIFFRACTION88
3.8492-3.91560.29371440.26133015X-RAY DIFFRACTION95
3.9156-3.98680.24631660.25333150X-RAY DIFFRACTION100
3.9868-4.06340.23651550.23293118X-RAY DIFFRACTION100
4.0634-4.14640.27251360.22243160X-RAY DIFFRACTION100
4.1464-4.23650.23861590.21253186X-RAY DIFFRACTION100
4.2365-4.3350.21731740.19393126X-RAY DIFFRACTION100
4.335-4.44340.21741620.18613135X-RAY DIFFRACTION100
4.4434-4.56350.20571430.17963149X-RAY DIFFRACTION100
4.5635-4.69780.19681540.17213164X-RAY DIFFRACTION100
4.6978-4.84940.20811570.17663178X-RAY DIFFRACTION100
4.8494-5.02260.21491400.17993165X-RAY DIFFRACTION100
5.0226-5.22360.22781650.17733138X-RAY DIFFRACTION100
5.2236-5.46120.2391920.18823123X-RAY DIFFRACTION100
5.4612-5.7490.22661730.19473140X-RAY DIFFRACTION100
5.749-6.10890.23581790.19593136X-RAY DIFFRACTION100
6.1089-6.58010.20391550.20693161X-RAY DIFFRACTION100
6.5801-7.24150.25751510.19453171X-RAY DIFFRACTION100
7.2415-8.28740.16671530.16513166X-RAY DIFFRACTION100
8.2874-10.43370.15841750.14193162X-RAY DIFFRACTION100
10.4337-63.49470.20671680.19283195X-RAY DIFFRACTION99
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)
11.1294-0.11820.20410.7236-0.02640.83540.0325-0.17970.51590.0371-0.02990.7806-0.2405-0.7982-0.05480.38010.1879-0.03370.9042-0.04211.1988359.66153.569157.8237
20.39110.0580.1180.7387-0.03560.76340.13430.0208-0.085-0.2610.02330.09480.33520.0371-0.05760.33690.048-0.06340.2055-0.05550.2593402.5771-18.207242.2353
30.73370.28590.04551.10030.80760.732-0.02760.1638-0.1578-0.17980.32330.04860.57190.00340.02150.9369-0.1281-0.38060.2147-0.02160.5541386.0544-43.963830.2098
40.5296-0.31230.57382.8355-2.12962.05080.14010.06860.1342-0.3352-0.20130.06060.183-0.14320.0651.3465-0.0849-0.32430.3650.16960.6432377.03425.5747-9.9525
50.42240.05520.1350.9645-0.07491.2047-0.06250.20520.0948-0.6217-0.00130.1518-0.12060.12570.0170.7982-0.2213-0.32710.40590.08920.516381.9205-19.519117.538
61.3603-0.3588-0.03020.42480.61481.2798-0.0367-0.20.4629-0.22280.0720.518-0.3125-0.6923-0.13470.5376-0.1334-0.18570.53620.03810.873365.9345-13.941949.4271
70.8371-0.29730.03820.89710.18130.7304-0.2118-0.11320.3898-0.0490.1824-0.0547-0.58-0.1147-0.19370.55350.15510.190.2625-0.15960.2825403.489838.630752.7598
80.7298-0.01760.860.4836-0.20521.81620.0489-0.02190.1064-0.19350.05820.2279-0.2205-0.3051-0.03290.56110.15010.03330.4250.01510.5074383.432231.464523.1435
92.5663-1.71040.02322.0012-0.22910.83720.0119-0.0111-0.340.15050.11530.8954-0.029-0.4370.0940.3780.140.14840.53-0.04060.5953386.216733.928354.3179
101.0914-0.220.18661.1841-0.15261.51330.03510.16490.2479-0.25470.01180.0654-0.34510.1619-0.03060.4404-0.01150.12570.2705-0.02440.3036407.6631.633727.6411
110.5103-0.24060.38980.7852-0.36050.38180.03190.14820.054-0.1492-0.0487-0.13650.17970.1449-0.01420.2862-0.0070.13360.3292-0.050.2344417.336513.170441.5974
120.4839-0.3031-0.22870.67090.03021.18620.1254-0.3385-0.01320.1039-0.11480.2653-0.0593-0.25920.01310.1727-0.00850.1570.5486-0.15460.3068402.14058.382673.8359
130.59120.24670.42920.7560.040.65830.0111-0.32380.2808-0.0761-0.00230.34010.257-0.0847-0.01520.1990.05390.02330.2978-0.10560.3293395.1834-7.01957.7943
144.27120.08470.34233.3261.87683.77220.01280.02910.11990.0428-0.0121-0.25290.19950.2375-0.04120.36280.3739-0.1150.8911-0.03840.5793447.3173-19.739864.91
150.7790.0570.0190.14-0.04820.3264-0.00250.2268-0.2802-0.0059-0.0612-0.09850.13150.1677-0.35210.16320.2612-0.13210.6682-0.16570.4117430.3729-12.720473.2037
161.20860.5609-0.27541.4975-0.19011.3050.0497-0.14140.04150.166-0.1121-0.08880.19740.3494-0.00650.15970.01160.0740.5919-0.09130.2061427.59661.108480.2808
170.8147-0.1870.03270.88060.1210.75440.1005-0.22210.00240.1837-0.0992-0.3675-0.0510.4758-0.04160.3116-0.0166-0.02720.5916-0.04910.318432.41610.385976.7217
181.4219-0.34930.71180.7871-0.47690.48530.0436-0.0325-0.3211-0.28620.0098-0.66230.19590.613-0.00790.66830.32970.03970.7832-0.19250.6545441.4385-22.894143.5604
191.26770.05960.5551.96330.53350.56810.2177-0.3455-0.01150.2855-0.0944-0.18330.27940.23080.01620.46170.1917-0.250.70330.04580.4634434.8533-22.5775.6069
200.92870.13530.3760.28990.3350.9362-0.21740.4731-0.0139-0.40430.13190.08240.1393-0.366-0.3441.4957-0.4473-0.90070.99980.16961.0872359.1079-26.8989-1.3407
211.15960.41230.29630.15540.03440.618-0.17770.30160.3935-0.10550.06190.2205-0.3165-0.08690.1891.415-0.4692-0.8551.33310.4181.4926349.3413-22.35155.8675
220.3444-0.1804-0.40750.09540.21750.49460.0295-0.15250.06230.4005-0.1395-0.3054-0.1760.12650.07961.29560.1983-0.29042.00760.30261.9811340.7193-16.85824.7686
230.6289-0.91560.02821.58980.5471.3920.2078-0.28470.41550.2627-0.11330.6002-0.4044-0.0627-0.04311.1602-0.1456-0.42541.03320.24511.4948349.2514-14.6287.8841
240.43130.2590.02530.9028-0.23360.90520.0614-0.07610.2134-0.2821-0.02370.71370.1516-0.43820.40040.7772-0.3897-0.57060.50250.05880.9917360.153-25.924623.3731
251.78770.1832-0.27761.64460.03251.32480.198-0.2471-0.0997-0.02590.04460.44940.273-0.2664-0.02620.5793-0.2837-0.13620.42810.03710.5138372.6432-36.894959.1504
264.03451.68112.40972.8311-0.92873.2380.1461-0.3113-0.2180.12750.0702-0.02930.14220.2715-0.06240.7852-0.2064-0.04740.58740.02960.6334384.4575-39.948872.2608
271.65441.04020.56430.685-0.0084.16330.0934-0.1906-0.21960.35160.11740.0320.061-0.2905-0.14350.817-0.1497-0.01610.50840.06990.5662371.3958-39.423661.9469
287.4701-3.4891.84925.5686-1.83013.45960.3139-0.1813-0.20590.10.14730.17610.2707-0.2821-0.2450.6238-0.31670.06030.4210.09190.7844369.5593-39.461354.6675
290.75560.0595-0.2731.03940.09130.5764-0.01420.3553-0.3621-0.2391-0.126-0.21280.3560.11920.05870.83130.59220.00110.6114-0.39630.9698430.2538-46.9129.9358
301.2604-2.5069-3.05476.46765.04518.2552-0.0962-0.1755-0.26190.2803-0.1159-0.14880.11130.0027-0.00431.36360.3715-0.22620.7907-0.06760.9072424.4039-52.102853.5163
317.8860.19170.19753.43850.4723.23330.0567-0.61960.33920.55140.2291-0.316-0.39130.3303-0.17741.40160.60090.09370.78930.15011.5249434.6864-54.822952.675
321.318-0.5841-0.49262.25460.36351.74890.00770.0575-0.22170.06260.0315-0.02630.26980.0216-0.12360.87770.2211-0.17330.5636-0.42060.7784421.5292-50.280336.39
334.81391.2733-0.15636.98740.56253.3141-0.14750.5386-0.5387-0.41750.1254-0.18240.41610.004-0.16611.08810.2058-0.12980.5457-0.38550.9156417.0544-53.706527.5002
340.5501-0.06440.98483.35750.60492.00910.02050.1353-0.56830.03710.00910.27820.2689-0.13030.08091.05730.4136-0.09650.5618-0.20470.7608422.7737-53.562234.9087
350.351-0.0609-0.27761.90860.24560.64710.1034-0.0095-0.1975-0.2796-0.03690.3492-0.2638-0.2605-0.0051.28310.0607-0.1250.4970.21650.5455374.773732.5611-9.111
362.12460.5682-0.6311.8021-0.45452.51720.26230.20470.01710.1491-0.11850.08660.0605-0.2656-0.00720.4425-0.02680.10490.50840.04320.3165407.271320.36921.2174
371.8144-0.7258-0.61762.0510.38670.58130.1507-0.0597-0.0177-0.00790.0298-0.0422-0.12490.14880.1850.15030.0920.14240.5202-0.08740.3069431.15423.416965.8582
383.2145-1.1706-2.65231.32490.13532.95630.0976-0.16490.64170.1917-0.0059-0.3714-0.95020.6837-0.05160.3682-0.12990.12710.6313-0.08880.7045438.92214.841961.1421
399.3986-0.63520.95198.776-5.89024.1023-0.1516-0.26310.5734-0.0023-0.17130.1153-0.7546-0.16540.29170.67060.18510.22681.1020.00970.9658444.868616.551354.9441
404.35521.3893-1.88833.7225-2.16563.9772-0.11990.03010.0047-0.0474-0.1781-0.31780.00980.23510.03240.2150.0070.13970.8579-0.02760.6038440.88054.616856.7419
411.4662-0.20710.08640.9021-0.53980.5437-0.0114-0.0479-0.0093-0.03280.0187-0.15750.03370.12350.0150.16740.10560.14910.3813-0.14230.3042430.43176.174657.9484
425.07131.66824.51032.6834-0.41675.74460.3321-0.23910.12160.2830.16830.1413-0.0938-0.00020.04320.2306-0.12570.00520.45270.02010.5435422.356723.654368.1383
430.6199-0.890.02073.47370.07760.62470.2818-0.3189-0.37790.2946-0.03580.38510.4342-0.0874-0.05530.56920.08-0.06060.4430.04160.3729416.2079-27.73675.0206
441.2395-0.1484-0.03072.4944-0.30040.89190.1264-0.3081-0.4464-0.11520.0575-0.33250.44860.30460.09950.53660.2463-0.20160.42980.06320.5044423.7873-35.307366.8844
451.0257-0.32840.25270.4210.23780.8560.2243-0.2038-0.32950.1070.0139-0.420.42340.62920.07280.38740.2744-0.08290.7841-0.01580.676442.5152-27.559773.041
462.312-1.21151.0265.54333.21473.35380.129-0.2123-0.01470.09760.02420.0634-0.1276-0.0649-0.06180.9946-0.0863-0.0371.1184-0.24231.0944408.282525.699986.4069
473.68053.4931.60093.43991.0932.18120.0224-0.0189-0.140.2534-0.0536-0.83560.03561.450.01521.5431-0.1636-0.11441.3582-0.05041.4328413.831531.698779.3527
486.2114-5.09773.29874.284-2.74712.1284-0.12960.04840.12610.32960.04650.62960.2401-0.7272-0.00881.56150.00960.05381.2297-0.50071.2795407.9429.504889.9156
490.00030.00410.00010.03660.00070.0087-0.1725-0.16-0.54110.1383-0.00450.37810.9408-0.58870.1562.30410.13960.0932.1856-0.03332.2886398.351330.550488.8106
502.7556-2.1051-0.48562.24751.13542.3486-0.1926-0.36150.49510.49480.2373-0.1428-0.5077-0.11450.01960.5954-0.09040.02550.7055-0.2030.3433411.442720.365582.894
511.880.3854-0.03694.2159-0.5842.3363-0.276-0.00980.60480.1414-0.09360.5653-0.7052-0.79830.35681.04980.26150.00150.94420.03450.7968388.39127.316957.2379
521.0613-0.3911.53475.1171-0.13722.2553-0.2681-0.1124-0.00770.77570.01190.645-0.4368-0.52160.15840.857-0.00070.14470.73870.02880.9199390.87268.542754.2398
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 394 )
2X-RAY DIFFRACTION2chain 'A' and (resid 395 through 889 )
3X-RAY DIFFRACTION3chain 'A' and (resid 890 through 1115 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1116 through 1280 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1281 through 1376 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1377 through 1448 )
7X-RAY DIFFRACTION7chain 'B' and (resid 20 through 185 )
8X-RAY DIFFRACTION8chain 'B' and (resid 186 through 408 )
9X-RAY DIFFRACTION9chain 'B' and (resid 409 through 487 )
10X-RAY DIFFRACTION10chain 'B' and (resid 488 through 700 )
11X-RAY DIFFRACTION11chain 'B' and (resid 701 through 820 )
12X-RAY DIFFRACTION12chain 'B' and (resid 821 through 994 )
13X-RAY DIFFRACTION13chain 'B' and (resid 995 through 1220 )
14X-RAY DIFFRACTION14chain 'C' and (resid 3 through 26 )
15X-RAY DIFFRACTION15chain 'C' and (resid 27 through 51 )
16X-RAY DIFFRACTION16chain 'C' and (resid 52 through 84 )
17X-RAY DIFFRACTION17chain 'C' and (resid 85 through 190 )
18X-RAY DIFFRACTION18chain 'C' and (resid 191 through 227 )
19X-RAY DIFFRACTION19chain 'C' and (resid 228 through 268 )
20X-RAY DIFFRACTION20chain 'E' and (resid 3 through 71 )
21X-RAY DIFFRACTION21chain 'E' and (resid 72 through 89 )
22X-RAY DIFFRACTION22chain 'E' and (resid 90 through 103 )
23X-RAY DIFFRACTION23chain 'E' and (resid 104 through 122 )
24X-RAY DIFFRACTION24chain 'E' and (resid 123 through 215 )
25X-RAY DIFFRACTION25chain 'F' and (resid 72 through 103 )
26X-RAY DIFFRACTION26chain 'F' and (resid 104 through 126 )
27X-RAY DIFFRACTION27chain 'F' and (resid 127 through 137 )
28X-RAY DIFFRACTION28chain 'F' and (resid 138 through 155 )
29X-RAY DIFFRACTION29chain 'H' and (resid 3 through 60 )
30X-RAY DIFFRACTION30chain 'H' and (resid 61 through 82 )
31X-RAY DIFFRACTION31chain 'H' and (resid 83 through 92 )
32X-RAY DIFFRACTION32chain 'H' and (resid 93 through 106 )
33X-RAY DIFFRACTION33chain 'H' and (resid 107 through 118 )
34X-RAY DIFFRACTION34chain 'H' and (resid 119 through 146 )
35X-RAY DIFFRACTION35chain 'I' and (resid 2 through 52 )
36X-RAY DIFFRACTION36chain 'I' and (resid 53 through 116 )
37X-RAY DIFFRACTION37chain 'J' and (resid 1 through 17 )
38X-RAY DIFFRACTION38chain 'J' and (resid 18 through 26 )
39X-RAY DIFFRACTION39chain 'J' and (resid 27 through 31 )
40X-RAY DIFFRACTION40chain 'J' and (resid 32 through 43 )
41X-RAY DIFFRACTION41chain 'J' and (resid 44 through 56 )
42X-RAY DIFFRACTION42chain 'J' and (resid 57 through 65 )
43X-RAY DIFFRACTION43chain 'K' and (resid 1 through 39 )
44X-RAY DIFFRACTION44chain 'K' and (resid 40 through 82 )
45X-RAY DIFFRACTION45chain 'K' and (resid 83 through 114 )
46X-RAY DIFFRACTION46chain 'L' and (resid 27 through 31 )
47X-RAY DIFFRACTION47chain 'L' and (resid 32 through 36 )
48X-RAY DIFFRACTION48chain 'L' and (resid 37 through 41 )
49X-RAY DIFFRACTION49chain 'L' and (resid 42 through 46 )
50X-RAY DIFFRACTION50chain 'L' and (resid 47 through 70 )
51X-RAY DIFFRACTION51chain 'T' and (resid 19 through 29 )
52X-RAY DIFFRACTION52chain 'R' and (resid 1 through 8 )

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