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- PDB-6bqf: Pol II elongation complex with 'dT-AP' at i+1, i-1 position -

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Basic information

Entry
Database: PDB / ID: 6bqf
TitlePol II elongation complex with 'dT-AP' at i+1, i-1 position
Components
  • (DNA-directed RNA polymerase II subunit ...) x 5
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • DNA (5'-D(P*CP*TP*(3DR)P*CP*TP*CP*TP*TP*GP*AP*TP*G)-3')
  • RNA (5'-R(*AP*UP*CP*AP*AP*GP*AP*GP*A)-3')
KeywordsTRANSFERASE/TRANSCRIPTION / Complex / DNA BINDING PROTEIN / DNA-RNA HYBRID / TRANSCRIPTION / TRANSFERASE-TRANSCRIPTION 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 / TP53 Regulates Transcription of DNA Repair Genes / termination of RNA polymerase II transcription / 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 / TP53 Regulates Transcription of DNA Repair Genes / termination of RNA polymerase II transcription / 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 Polymerase II Pre-transcription Events / RNA-templated transcription / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / transcription initiation at RNA polymerase III promoter / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / termination of RNA polymerase I transcription / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / Estrogen-dependent gene expression / transcription by RNA polymerase III / RNA polymerase II activity / Dual incision in TC-NER / transcription elongation by RNA polymerase I / transcription-coupled nucleotide-excision repair / tRNA transcription by RNA polymerase III / RNA polymerase I complex / RNA polymerase I activity / RNA polymerase III complex / translesion synthesis / RNA polymerase II, core complex / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / 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 / nucleus / metal ion binding / 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 / Gyrase A; domain 2 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / 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. / Homeodomain-like / 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 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, subunit RPB6 / 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 / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / 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 / 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 / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / 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 / RNA polymerases D / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4
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: 3.35 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 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_audit_support.funding_organization
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*CP*TP*(3DR)P*CP*TP*CP*TP*TP*GP*AP*TP*G)-3')
R: RNA (5'-R(*AP*UP*CP*AP*AP*GP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)481,86321
Polymers481,31512
Non-polymers5489
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area61210 Å2
ΔGint-394 kcal/mol
Surface area136090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.400, 221.350, 193.700
Angle α, β, γ (deg.)90.00, 100.60, 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 / 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 / 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 / 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 / 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 / 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 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 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 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 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 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*CP*TP*(3DR)P*CP*TP*CP*TP*TP*GP*AP*TP*G)-3')


Mass: 8770.637 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#12: RNA chain RNA (5'-R(*AP*UP*CP*AP*AP*GP*AP*GP*A)-3')


Mass: 2918.831 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: 3.69 Å3/Da / Density % sol: 66.66 %
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: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.35→82.8 Å / Num. obs: 92041 / % possible obs: 99.9 % / Redundancy: 3.7 % / Net I/σ(I): 6.5
Reflection shellResolution: 3.35→3.53 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 3.35→82.763 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.84
RfactorNum. reflection% reflection
Rfree0.2446 4549 4.94 %
Rwork0.2171 --
obs0.2184 92012 92.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.35→82.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27808 426 9 0 28243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00228794
X-RAY DIFFRACTIONf_angle_d0.53438969
X-RAY DIFFRACTIONf_dihedral_angle_d11.37310984
X-RAY DIFFRACTIONf_chiral_restr0.0214383
X-RAY DIFFRACTIONf_plane_restr0.0024970
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3501-3.38810.414340.3045749X-RAY DIFFRACTION23
3.3881-3.4280.2876740.28621404X-RAY DIFFRACTION45
3.428-3.46980.3042940.3031873X-RAY DIFFRACTION59
3.4698-3.51370.29411180.29522165X-RAY DIFFRACTION69
3.5137-3.560.35491220.29132537X-RAY DIFFRACTION80
3.56-3.60870.32331630.29662795X-RAY DIFFRACTION90
3.6087-3.66030.29571560.28713186X-RAY DIFFRACTION99
3.6603-3.71490.30331630.27463121X-RAY DIFFRACTION100
3.7149-3.7730.32841490.27063202X-RAY DIFFRACTION100
3.773-3.83480.29231850.26133105X-RAY DIFFRACTION100
3.8348-3.9010.26941340.25973172X-RAY DIFFRACTION100
3.901-3.97190.26891580.25183215X-RAY DIFFRACTION100
3.9719-4.04830.26061750.2283114X-RAY DIFFRACTION100
4.0483-4.13090.26071600.22373159X-RAY DIFFRACTION100
4.1309-4.22070.24941680.20933202X-RAY DIFFRACTION100
4.2207-4.31890.25861550.20173162X-RAY DIFFRACTION100
4.3189-4.42690.2131640.19683126X-RAY DIFFRACTION100
4.4269-4.54660.22491660.1913170X-RAY DIFFRACTION100
4.5466-4.68040.2191700.18373167X-RAY DIFFRACTION100
4.6804-4.83140.21451720.17973176X-RAY DIFFRACTION100
4.8314-5.00410.23961530.18983165X-RAY DIFFRACTION100
5.0041-5.20440.23011700.18683141X-RAY DIFFRACTION100
5.2044-5.44120.2371730.19713183X-RAY DIFFRACTION100
5.4412-5.7280.20991550.20123147X-RAY DIFFRACTION100
5.728-6.08680.23211790.20973169X-RAY DIFFRACTION100
6.0868-6.55660.24821590.21573154X-RAY DIFFRACTION99
6.5566-7.21610.23751660.19853148X-RAY DIFFRACTION99
7.2161-8.25940.18771710.183170X-RAY DIFFRACTION99
8.2594-10.40280.16311560.15113181X-RAY DIFFRACTION99
10.4028-82.78840.22021870.20413205X-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)
10.03790.0119-0.01030.0057-0.00120.01290.0467-0.02980.13150.0581-0.0820.1791-0.0333-0.1386-0.01520.05280.1627-0.04960.309-0.08650.4921288.090734.1579438.1063
20.00050.0784-0.03020.0538-0.00780.36710.2729-0.1153-0.3474-0.09330.10680.01740.38610.05060.74340.10120.20760.0315-0.2747-0.1974-0.1144333.472613.6051423.4628
30.06440.0480.05630.05270.01240.0670.06340.0713-0.0994-0.12120.09950.00810.3296-0.01880.12310.5428-0.0781-0.31660.0309-0.09090.3528312.909-11.0783412.3268
4-0.0025-0.00040.00540.0240.02380.01940.03390.01780.05890.0035-0.0305-0.00130.058-0.00820.00090.80550.0113-0.21320.19530.12250.4121305.74235.8261370.4081
50.11720.04540.06290.05140.00790.0553-0.0497-0.04150.1079-0.1902-0.01120.13990.0069-0.0784-0.07430.2265-0.1009-0.20060.12860.04770.3176303.972913.6198410.7963
60.009-0.00430.0060.0239-0.02330.0310.0842-0.06880.1393-0.08320.0370.0461-0.13560.01420.10350.31080.14240.19960.0594-0.14230.2196329.876964.982430.2053
70.07450.0101-0.00410.0260.00220.01010.0381-0.03840.1715-0.08420.04350.128-0.1103-0.07770.12640.18340.25510.1630.1770.00630.2576312.370761.2708410.0567
80.0369-0.0124-0.03260.0243-0.04530.11710.02930.00260.0777-0.0621-0.01360.0165-0.10530.1450.01060.2380.03620.25420.14670.00560.085339.977159.3689407.181
90.0133-0.02570.04690.0227-0.03530.05640.0853-0.10240.00410.178-0.0040.0552-0.0615-0.02680.06790.02040.07350.28840.126-0.2555-0.0765333.628940.3615451.0498
100.020.02210.0570.1380.03930.12260.025-0.08480.039-0.0298-0.03270.22940.117-0.07710.007-0.11830.14980.08120.2963-0.15530.2972323.551123.6434438.4551
110.0031-0.00240.00020.001-0.0002-0-0.0060.00390.00140.0053-0.0093-0.00070.01040.0112-00.230.146-0.08740.4405-0.02770.398375.520410.8997445.8929
120.02140.0155-0.02010.0126-0.01690.023-0.01250.0089-0.05380.004-0.0217-0.0150.02250.0288-0.00740.19390.1116-0.11490.3783-0.08250.277358.640717.9547454.0698
130.00490.0055-0.00170.0034-0.00380.00510.0143-0.00560.00010.0127-0.0022-0.0060.01620.03560.0217-0.0059-0.0016-0.0030.182-0.05910.075355.790231.7756461.1139
140.01330.00590.00090.0157-0.00280.00150.0179-0.04120.01650.02910.0371-0.01630.02670.05990.03940.1127-0.0476-0.12690.3308-0.04110.1437360.00437.6311464.0388
150.00610.0083-0.00820.00780.00410.00680.02390.0526-0.0177-0.0385-0.0245-0.06520.02870.0607-0.00230.18030.10130.00930.3234-0.10170.2562364.761614.2441432.7512
160.00780.00010.0030.00950.00450.00130.04740.0041-0.02540.01840.0335-0.04810.05050.01730.01330.2270.1786-0.08120.34790.03790.2744365.75465.3203447.4739
170.00310.00170.0019-0.00010.00090.00270.00810.0329-0.0123-0.0176-0.0077-0.02920.0065-0.0035-00.6568-0.1605-0.34660.56750.05860.5708290.36834.8445377.0702
180.00260.00270.00250.00160.00130.0014-0.00260.01190.01330.0042-0.01980.00520.0084-0.011100.7334-0.0962-0.17610.7114-0.00460.7571280.2045-1.7518386.1315
190.00260.00120.00170.0004-0.00040.00030.00880.0095-0.0036-0.00350.00140.0027-0.0134-0.001900.9291-0.0257-0.07670.99190.06241.013278.1847.8672386.1662
200.0026-0.00020.00150.00020.00050.00050.01440.00630.0135-0.0039-0.001-0.004-0.02220.0044-00.9019-0.0219-0.0740.97690.09911.0326273.724314.2065388.1507
210.00540.00130.00140.00370.00760.0143-0.0241-0.01850.0189-0.014-0.0510.0680.0059-0.0667-0.02730.3089-0.1804-0.26050.2156-0.00680.4556290.1533.8119404.5418
22-0.00010.00020.00030.0008-0.00020.00030.0030.0014-0.0034-0.00770.0115-0.00940.00740.0026-00.4592-0.0632-0.03830.44750.04240.5084294.5024-11.0117432.357
230.00080.0005-0.00080.0008-0.00060.00090.0118-0.0215-0.0067-0.0019-0.00630.00790.0043-0.002400.3168-0.07240.00260.3293-0.01560.3021306.4545-1.9527446.2667
240-0.00010.00020.0005-00.0006-0.0078-0.0042-0.00470.004-0.01030.00470.00330.001-00.7366-0.0441-0.070.701-0.02690.7092312.4862-9.8861456.4675
250-00.00030.0004-0.00040.00110.00050.0022-0.00550.00260.0054-0.00470.00050.001200.5237-0.09390.01360.40150.02010.4426309.594-10.1467448.4043
260.0035-0.00150.00110.002-0.00060.00030.0014-0.00130.0009-0.00030.00210.0020.00450.003600.4506-0.0093-0.0070.45270.01340.4474294.7088-4.1805437.7706
270.00050.00020.00020.0006-0.00060.00020.00980.00390.0020.00170.00020.00180.0029-0.007500.5725-0.06590.00220.60740.03050.6797291.7258-5.4207433.4842
280.00270.0007-0.00120.0008-0.00050.00090.005-0.0049-0.001-0.0040.0112-0.00490.0060.00400.4213-0.0415-0.04750.36960.02630.4359305.6136-12.8065437.6403
290.0008-0.0016-0.00160.0012-0.00010.0006-0.01150.0147-0.00180.0014-0.0033-0.00210.00870.011600.75910.11860.0610.645-0.11150.7744358.3457-21.6017410.7064
300.0001-0.0003-0.00090.0006-0.00010.0013-0.0175-0.00040.0131-0.0073-0.0026-0.00420.00430.0058-00.48810.1631-0.0040.4693-0.08430.5141356.2843-7.0923410.9575
310.0018-0.00070.00160.00110.00090.001-0.00860.01320.0046-0.00340.0093-0.00150.0032-0.006300.52660.12890.00390.4961-0.11290.5614355.8289-20.5239407.3384
320.0012-0.0011-0.00060.00110.00170.004-0.010.00260.0037-0.0010.0074-0.0109-0.00080.001-00.4160.1025-0.02210.4622-0.07240.4472364.805-10.7627413.7998
330.0006-0.00220.00050.0019-0.0010.00040.00010.0023-0.013-0.0135-0.0093-0.00430.00650.007100.57020.08040.00710.4319-0.10420.5282355.3557-22.1423427.3965
34-0-0.0006-0.00040.00040.0010.00190.0042-0.0087-0.0025-0.0039-0.00260.00030.00040.0013-00.76780.07650.0140.74270.02790.7847362.7351-24.2639433.7826
350.0004-0.0015-0.00060.00290.00260.00080.0009-0.00680.00500.0079-0.01010.0076-0.0018-00.5960.0303-0.02730.5043-0.24410.5784349.841-19.6614417.4158
360.0015-0.00170.00060.00130.00090.0007-0.0077-0.00420.00710.00810.0051-0.0066-0.00530.000600.57330.0609-0.0250.497-0.08820.5605345.3105-23.0833408.5684
370.0007-0.00090.00080.00170.00050.0017-0.0016-0.00230.0020.00450.00950.0042-0.0014-0.0079-00.60690.0907-0.0540.5385-0.05880.5294349.2971-17.1392411.6813
38-0.00020-00.0004-0.00020.00010.0052-0.0052-0.00570.00130.00180-0.0029-0.004100.75150.0088-0.00150.678-0.05010.7142345.958-27.7252416.7036
390.0032-0.0003-0.00130.00060.00030.0003-0.00290.00320.00130.0032-0.01180.003600.008500.65050.05780.02540.5975-0.04950.6409361.0461-21.7132419.5036
400.0005-0.00020.0020.00640.00120.00230.01650.0241-0.0196-0.00830.02110.0072-0.0118-0.0259-00.63980.0477-0.15030.31990.16490.4751303.189162.7263371.5371
410.00410.00770.00070.0109-0.00030.00030.03010.01350.0013-0.00230.0144-0.00310.0225-0.00330.03860.248-0.0170.10020.31750.02180.1022335.697150.839381.8999
420.00110.0016-0.00160.0011-0.00160.00020.0328-0.0017-0.00670.00210.02370-0.01320.007300.157-0.01850.06180.3683-0.0730.2903359.452434.1132446.653
430.001-0.0004-0.00040.0004-0.00030.0009-0.0086-0.00530.0030.002-0.0057-0.0006-0.00470.0023-00.236-0.03740.08510.3283-0.06360.314367.137445.5082441.97
440.00140.00240.00150.00660.00370.00210.00010.00060.00220.0004-0.0027-0.0013-0.00420.001800.5355-0.01320.0130.58670.0210.5779373.207346.975435.8844
450.00120.0003-0.0004-0.0001-0.0002-0.0002-0.0160.004-0.00130.0026-0.00750.0014-0.00130.0114-00.1683-0.01130.12230.3030.04280.2678369.15435.2239437.6462
46-0.0002-0.00030.00010.00140.0006-0.00020.0138-0.0067-0.00940.00270.0011-0.0126-0.01650.004300.16480.050.09740.2948-0.04280.1609358.681536.7628438.7941
470.0008-0.00010.00010.0004-0.00020.00010.00180.00310.00840.00760.0045-0.0059-0.00160.001100.1496-0.02840.06950.223-0.0240.2274350.656954.2027448.8391
480.0009-0.00190.00550.0009-0.00050.00310.052-0.0333-0.0049-0.00540.00540.01320.03260.0382-00.2550.0634-0.05250.2710.03850.2292344.47062.9499455.8315
490.0008-0.00160.00090.00350.00160.0001-0.0079-0.0104-0.008-0.005-0.0074-0.01220.00050.0075-0.00080.19550.1173-0.04930.17880.01370.2419358.5207-4.3911446.9549
500.004-0.00270.00450.0050.00310.00650.0023-0.0147-0.023-0.0012-0.0118-0.00680.01460.0121-0.00320.22710.1034-0.17790.19550.07040.1974348.4128-4.7692448.2386
510.0043-0.00630.00290.0059-0.0051-0.00070.0415-0.01270-0.00250.0599-0.01470.04910.046200.34230.1398-0.05540.53030.07520.553370.71023.0669454.051
520.00040.0006-0.0010.0008-0.00090.00130.00490.0038-0.0004-0.0087-0.0025-0.005700.001700.72040.0007-0.00570.7072-0.06750.7065339.117559.0262463.9665
530.0383-0.0008-0.009200.00030.003700.0003-0.0019-00.0013-0.00150.00010.00010.00010.7666-0.01040.00810.7231-0.08030.7451336.219660.2108470.3433
540.01740.0184-0.02660.0197-0.02830.0408-0.002-0.00030.0011-0.0006-0.0004-0.0001-0.00020.0008-01.52330.0109-0.00331.5262-0.01591.5232326.789161.1851469.3878
55-0.0008-0.0026-0.00150.00150.00350.00170.0022-0.0020.0054-0.00350.00020.0068-0.03440.0438-00.25080.01020.05720.3032-0.10430.1603339.718750.9886463.5703
56-0.00070.0019-0.0003-0.0005-0.00050.0002-0.0375-0.00780.00520.019-0.011-0.0176-0.0040.0219-00.99510.03010.03291.04680.110.9927315.658639.5231438.276
570.0004-0.00010.00070.0010.00130.0013-0.0026-0.00470.02080.00450.00120.0209-0.0261-0.0075-01.1597-0.0958-0.02451.13920.05091.1739318.227739.447435.8486
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 844 )
3X-RAY DIFFRACTION3chain 'A' and (resid 845 through 1116 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1117 through 1280 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1281 through 1446 )
6X-RAY DIFFRACTION6chain 'B' and (resid 20 through 241 )
7X-RAY DIFFRACTION7chain 'B' and (resid 242 through 533 )
8X-RAY DIFFRACTION8chain 'B' and (resid 534 through 776 )
9X-RAY DIFFRACTION9chain 'B' and (resid 777 through 994 )
10X-RAY DIFFRACTION10chain 'B' and (resid 995 through 1220 )
11X-RAY DIFFRACTION11chain 'C' and (resid 3 through 26 )
12X-RAY DIFFRACTION12chain 'C' and (resid 27 through 51 )
13X-RAY DIFFRACTION13chain 'C' and (resid 52 through 84 )
14X-RAY DIFFRACTION14chain 'C' and (resid 85 through 162 )
15X-RAY DIFFRACTION15chain 'C' and (resid 163 through 209 )
16X-RAY DIFFRACTION16chain 'C' and (resid 210 through 268 )
17X-RAY DIFFRACTION17chain 'E' and (resid 3 through 54 )
18X-RAY DIFFRACTION18chain 'E' and (resid 55 through 71 )
19X-RAY DIFFRACTION19chain 'E' and (resid 72 through 89 )
20X-RAY DIFFRACTION20chain 'E' and (resid 90 through 130 )
21X-RAY DIFFRACTION21chain 'E' and (resid 131 through 215 )
22X-RAY DIFFRACTION22chain 'F' and (resid 72 through 86 )
23X-RAY DIFFRACTION23chain 'F' and (resid 87 through 103 )
24X-RAY DIFFRACTION24chain 'F' and (resid 104 through 116 )
25X-RAY DIFFRACTION25chain 'F' and (resid 117 through 132 )
26X-RAY DIFFRACTION26chain 'F' and (resid 133 through 137 )
27X-RAY DIFFRACTION27chain 'F' and (resid 138 through 147 )
28X-RAY DIFFRACTION28chain 'F' and (resid 148 through 155 )
29X-RAY DIFFRACTION29chain 'H' and (resid 3 through 16 )
30X-RAY DIFFRACTION30chain 'H' and (resid 17 through 30 )
31X-RAY DIFFRACTION31chain 'H' and (resid 31 through 43 )
32X-RAY DIFFRACTION32chain 'H' and (resid 44 through 53 )
33X-RAY DIFFRACTION33chain 'H' and (resid 54 through 82 )
34X-RAY DIFFRACTION34chain 'H' and (resid 83 through 92 )
35X-RAY DIFFRACTION35chain 'H' and (resid 93 through 106 )
36X-RAY DIFFRACTION36chain 'H' and (resid 107 through 118 )
37X-RAY DIFFRACTION37chain 'H' and (resid 119 through 127 )
38X-RAY DIFFRACTION38chain 'H' and (resid 128 through 140 )
39X-RAY DIFFRACTION39chain 'H' and (resid 141 through 146 )
40X-RAY DIFFRACTION40chain 'I' and (resid 2 through 52 )
41X-RAY DIFFRACTION41chain 'I' and (resid 53 through 116 )
42X-RAY DIFFRACTION42chain 'J' and (resid 1 through 17 )
43X-RAY DIFFRACTION43chain 'J' and (resid 18 through 26 )
44X-RAY DIFFRACTION44chain 'J' and (resid 27 through 31 )
45X-RAY DIFFRACTION45chain 'J' and (resid 32 through 43 )
46X-RAY DIFFRACTION46chain 'J' and (resid 44 through 56 )
47X-RAY DIFFRACTION47chain 'J' and (resid 57 through 65 )
48X-RAY DIFFRACTION48chain 'K' and (resid 1 through 39 )
49X-RAY DIFFRACTION49chain 'K' and (resid 40 through 55 )
50X-RAY DIFFRACTION50chain 'K' and (resid 56 through 82 )
51X-RAY DIFFRACTION51chain 'K' and (resid 83 through 114 )
52X-RAY DIFFRACTION52chain 'L' and (resid 27 through 36 )
53X-RAY DIFFRACTION53chain 'L' and (resid 37 through 41 )
54X-RAY DIFFRACTION54chain 'L' and (resid 42 through 46 )
55X-RAY DIFFRACTION55chain 'L' and (resid 47 through 70 )
56X-RAY DIFFRACTION56chain 'T' and (resid 18 through 29 )
57X-RAY DIFFRACTION57chain 'R' and (resid 1 through 9 )

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