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

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Basic information

Entry
Database: PDB / ID: 6blp
TitlePol II elongation complex with an abasic lesion at i+1 position, soaking AMPCPP
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 / cytoplasmic stress granule / peroxisome / ribosome biogenesis / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
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, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit Rpo11 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerases L / 13 to 16 Kd subunits signature. / Homeodomain-like / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Single Sheet / Nucleic acid-binding proteins / Beta Complex / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / 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
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / 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 ...DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / 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: 3.203 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 11, 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)482,07223
Polymers480,99512
Non-polymers1,07711
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area61650 Å2
ΔGint-398 kcal/mol
Surface area136070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.060, 222.180, 193.200
Angle α, β, γ (deg.)90.00, 101.34, 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 3 / RNA polymerase II subunit B3 / B44.5 / DNA-directed RNA polymerase II ...RNA polymerase II subunit 3 / RNA polymerase II subunit B3 / B44.5 / DNA-directed RNA polymerase II 45 kDa polypeptide


Mass: 35330.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / 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 / 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


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 / 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 , 4 types, 12 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.: 2 / Source method: obtained synthetically / Formula: Mg
#15: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#16: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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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: 3.7 Å3/Da / Density % sol: 66.74 %
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 S 6M / 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: 3.2→82.9 Å / Num. obs: 99794 / % possible obs: 99.4 % / Redundancy: 3.5 % / Net I/σ(I): 5.3

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 3.203→82.88 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2567 4881 4.89 %
Rwork0.2144 --
obs0.2164 99769 87.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.203→82.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27808 389 41 1 28239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00228804
X-RAY DIFFRACTIONf_angle_d0.53138981
X-RAY DIFFRACTIONf_dihedral_angle_d11.62410987
X-RAY DIFFRACTIONf_chiral_restr0.0214381
X-RAY DIFFRACTIONf_plane_restr0.0024973
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.203-3.23940.360290.3109205X-RAY DIFFRACTION6
3.2394-3.27760.3633360.3518646X-RAY DIFFRACTION18
3.2776-3.31750.2945640.30871302X-RAY DIFFRACTION36
3.3175-3.35950.3828870.31471850X-RAY DIFFRACTION51
3.3595-3.40370.30931000.29782346X-RAY DIFFRACTION63
3.4037-3.45040.34181340.29212570X-RAY DIFFRACTION72
3.4504-3.49960.33661650.28242961X-RAY DIFFRACTION82
3.4996-3.55190.351840.28383255X-RAY DIFFRACTION91
3.5519-3.60740.34531900.2833565X-RAY DIFFRACTION99
3.6074-3.66650.31682000.27013595X-RAY DIFFRACTION100
3.6665-3.72980.31371850.25873614X-RAY DIFFRACTION100
3.7298-3.79760.29661940.25413642X-RAY DIFFRACTION100
3.7976-3.87060.29691760.25293663X-RAY DIFFRACTION100
3.8706-3.94960.30491690.24053615X-RAY DIFFRACTION100
3.9496-4.03550.25241850.22663598X-RAY DIFFRACTION100
4.0355-4.12940.3021860.2113640X-RAY DIFFRACTION100
4.1294-4.23260.25771890.20053601X-RAY DIFFRACTION100
4.2326-4.34710.21431930.18883630X-RAY DIFFRACTION100
4.3471-4.4750.24471760.18023597X-RAY DIFFRACTION100
4.475-4.61940.24111900.16973603X-RAY DIFFRACTION100
4.6194-4.78450.22261900.16473641X-RAY DIFFRACTION100
4.7845-4.9760.20961600.17273673X-RAY DIFFRACTION100
4.976-5.20250.21271800.183616X-RAY DIFFRACTION100
5.2025-5.47670.22041920.18863624X-RAY DIFFRACTION100
5.4767-5.81980.22951890.20213625X-RAY DIFFRACTION100
5.8198-6.2690.25211940.20813632X-RAY DIFFRACTION100
6.269-6.89950.25322000.21163596X-RAY DIFFRACTION100
6.8995-7.89730.21011870.18833650X-RAY DIFFRACTION100
7.8973-9.9470.17371870.15953647X-RAY DIFFRACTION99
9.947-82.90750.21841900.20073686X-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)
10.00730.0030.00360.0347-0.00610.01030.05840.00130.15170.0339-0.03790.1524-0.0185-0.16380.02870.02520.1332-0.01030.3579-0.02580.3761491.29370.3133246.2342
20.1781-0.01150.00290.1145-0.10860.50780.2715-0.0052-0.2836-0.09170.06090.02740.4001-0.05090.97540.08920.12760.0386-0.288-0.2697-0.1409532.9522-25.4847228.9335
30.11840.051-0.00210.10710.09940.09270.01020.05170.0135-0.05610.05650.01680.1154-0.02260.12760.3674-0.062-0.18070.04310.01410.2169517.1668-35.7124216.0393
40.00340.00660.00520.00830.00750.0070.0221-0.0051-0.0002-0.0084-0.0169-0.00190.03550.00840.00090.5950.0505-0.15610.22840.08840.3976507.75795.9853176.0097
50.00760.003-0.00250.00350.0010.0016-0.01350.00070.0081-0.046-0.00670.0120.00750.003-0.05590.2733-0.0928-0.15040.10620.05720.1719514.249-22.9222206.4507
60.00850.00620.00120.0033-0.00050.0007-0.0041-0.03440.0244-0.0233-0.03990.0319-0.0126-0.080700.1460.0094-0.03630.22850.0160.3256497.8252-17.1801237.9987
70.0307-0.0049-0.00220.0050.01320.0392-0.052-0.00520.0470.04580.03280.0295-0.1356-0.0755-0.02610.20060.11420.17390.1071-0.11670.185535.208435.538241.7765
80.02320.0102-0.00310.0489-0.04010.04790.09320.020.0777-0.0673-0.00170.0786-0.0538-0.03070.15870.2110.18290.06520.18070.05240.2333515.47428.1867212.0507
90.015-0.03360.00410.13270.02720.04390.0255-0.00480.00550.00630.03430.0045-0.0036-0.01060.10670.14280.1070.08760.1823-0.07550.2085517.911330.7969243.1756
100.01250.0042-0.03630.0313-0.03690.03470.03530.03040.1205-0.0783-0.0150.0072-0.13540.0566-0.03450.02510.02950.24460.0345-0.0188-0.0426542.117323.701217.576
110.02690.00130.00410.0403-0.07730.1530.118-0.10130.07320.1030.02460.0309-0.0486-0.02330.24330.03040.0890.18870.178-0.20560.0202536.89996.6549259.3642
120.02330.01760.06510.1193-0.00860.1490.0264-0.05190.0265-0.0408-0.00690.09410.0466-0.04270.02190.03010.0680.03070.2867-0.08060.2081526.9355-10.1149246.7282
130.0016-0.00140.00050.00060.00010-0.0197-0.00030.00850.0134-0.0107-0.008-0.00690.0013-00.21990.1601-0.0460.4667-0.00550.3633579.0061-22.7198254.4878
140.0024-0.00260.00220.001-0.00170.00210.00860.0209-0.0480.00310.0065-0.00770.01490.01780.00310.10780.1102-0.04040.1822-0.07630.115561.9505-15.6954262.57
150.0053-0.0036-0.00010.0054-0.00720.00970.00130.0072-0.00150.0122-0.00790.00110.00830.0449-0.02130.05840.0054-0.00370.2334-0.0450.0733558.7881-2.619273.5463
160.00830.01530.00930.02720.01210.01190.0471-0.0445-0.01370.01210.0076-0.01420.03270.02690.0530.04550.0086-0.07090.2212-0.03610.1253563.98773.5518268.5473
170.0006-0.001-0.0004-0.00040.00050.00040.0081-0.01120.0082-0.00760.0081-0.0162-0.00270.01030.01140.13220.12950.04540.2964-0.08850.2194570.9874-21.6443234.7789
180.0193-0.00820.0070.00830.00150.00470.0283-0.0009-0.00150.00620.0097-0.01310.03590.00840.02490.10310.1238-0.05160.20270.02440.1428569.225-28.3279255.994
190.00210.0030.00180.00240.00330.00390.02750.0383-0.0056-0.0223-0.0159-0.02230.0073-0.0256-00.7205-0.184-0.32820.62630.01190.6361492.5356-29.2714185.7244
200.00040.00050.00070.00020.00060.0009-0.00380.0024-0.0026-0.0004-0.00590.00610.0049-0.0057-00.6549-0.0555-0.08220.68970.02060.6976482.2104-36.3205200.1294
210.0011-0.00050.00070.0001-0.00030.0005-0.00210.00630.0041-0.0013-0.0050.0008-0.00620.0002-01.08480.0316-0.04041.11840.0651.1203476.3111-18.633191.2808
220.0019-00.0011-0.000100.00010.0134-0.0040.0065-0.00380.00440.0005-0.00420.006800.6552-0.0204-0.05380.69050.07670.7375481.8468-18.234196.1449
230.00150.0029-0.00050.0001-0.00390.00560.0059-0.03020.02070.0025-0.04230.041-0.0054-0.0428-0.00490.2262-0.167-0.21940.19570.04580.3635492.4724-29.347211.9324
240.00060.00060.00050.0006-0.00050.00050.00060.0041-0.0050.00750.0031-0.0019-0.00210.001-00.5149-0.0874-0.09160.50320.04020.518498.0562-44.8467240.3785
250.0010.00170.00020.00160.00050.0005-0.0072-0.0188-0.0055-0.00010.00470.00730.0061-0.0003-00.35-0.11320.00130.33220.05730.3446509.8408-35.7722254.3837
260.0001-0.0002-0.00050.00030.00020.0010.0059-0.003-0.00170.00550.00760.0024-0.0006-0.004700.5332-0.0514-0.04120.4970.01310.4845515.812-43.6246264.5987
270.00030.00030.00030.0009-0.00020.00020.00440.0021-0.0064-0.0005-0.0018-0.00150.00070.00300.4384-0.09240.04660.3250.0270.3588513.0342-43.9108256.4729
280.0012-0.00010.00070.0008-0.0010.00110.00650.00360.00270.00570.00610.00330.0054-0.005100.39280.00140.00520.41750.0320.4438495.7911-36.5634242.3582
290.009-0.00580.00310.0045-0.00220.00110.0016-0.00210.00030.0004-0.0005-0.00130.00230.00200.6107-0.044-0.01280.58060.02930.6032497.1067-42.6668244.3494
300.00410.002-0.00250.0011-0.00120.00140.0062-0.0076-0-0.00440.0088-0.0070.0068-0.001200.3137-0.0642-0.01830.24550.02820.297509.1209-46.6206245.783
310.0007-0.0006-0.00040.000200-0.00220.01030.0028-0.0017-0.0017-0.00440.00630.005900.49390.12620.04380.4487-0.07470.5068562.2072-55.2667219.1908
320.0002-0.0006-0.00020.001-0.00020.0011-0.0076-0.00140.0095-0.00730.0012-0.00190.00660.0048-00.49840.1349-0.00160.4551-0.04610.5468560.1515-40.745219.4633
330.0023-0.00130.00240.0010.00060.0014-0.02140.00890.0002-0.00580.0091-0.00870.0065-0.0126-00.48550.1625-0.03540.4523-0.07950.5263559.6938-54.1403215.7209
340.0013-0.0012-0.00090.00150.00260.0054-0.00920.0050.00180.00220.0035-0.0063-0.00070.001-00.40320.1008-0.00410.4365-0.06960.4413568.6729-44.3796222.2561
350.0006-0.00160.00050.0017-0.00070.0001-0.00190.0014-0.0176-0.0160.00670.00190.00320.0019-00.34910.09580.01430.2715-0.06670.3534559.0564-55.717235.8349
360-0.0005-0.00050.00060.00150.00530.0067-0.0091-0.0005-0.0013-0.0034-0.0006-0.00070.0025-00.66950.08350.02050.6280.0170.6853566.444-57.8479242.2137
370.0011-0.0021-0.00110.00310.00210.00090.0048-0.0030.0042-0.00410.0128-0.01280.0014-0.0027-00.47720.0896-0.02410.3811-0.16120.4663553.6213-53.2387225.8627
380.0004-0.00040.00080.0010.00050.001-0.01370.0039-0.00730.00660.0014-0.0038-0.0041-0.0032-00.71240.0595-0.05890.6316-0.07050.6685549.2089-56.6672216.9352
390.001-0.0010.00080.0020.00150.0027-0.0028-0.00230.00080.00050.01480.0048-0.0003-0.01-00.48170.1144-0.05780.4463-0.04810.4233553.1426-50.7866220.1399
40-0-0.00030.00020.0003-00.00020.0041-0.0055-0.0102-0.00290.0047-0.0030.0018-0.0051-00.55980.0392-0.00870.4849-0.050.5429549.75-61.3182225.107
410.0088-0.0007-0.00370.00060.00010.0015-0.00410.0033-0.00150.0016-0.00470.0082-0.00280.0088-00.51740.07690.01030.479-0.04760.5204564.8473-55.292227.9353
42-0.0009-0.00110.00160.0031-0.00170.00110.00920.0084-0.007-0.01840.02620.0116-0.0179-0.010600.59470.048-0.10010.28020.13620.4226506.982429.0958179.9691
430.00420.00060.00470.0057-0.00320.00710.00810.0118-0.0063-0.0098-0.0016-0.00010.002-0.00640.00910.18730.01220.07930.2230.05250.0685539.564217.2414190.4234
440.00070.0003-0.00050.0009-0.00010-0.002-0.0032-0.0005-0.00220.00250.0017-0.00180.0082-00.151-0.01050.03960.2746-0.05330.2273561.6224-0.2569254.9565
450.0006000.00020.00010.0004-0.0077-0.00380.0044-0.0061-0.00460.0028-0.009-0.0016-00.2613-0.00940.06230.3408-0.10090.3507570.21310.2647251.7777
460.0025-0.00280.00430.0025-0.00480.0082-0.0182-0.0015-0.0091-0.0008-0.0294-0.0217-0.02230.0268-0.00030.14720.0430.07670.372-0.01610.2541568.51834.4109246.4091
470.0006-0.0003-00.0005-0.00020.00020.00890.0065-0.00420.00490.0111-0.00270.0029-0.000700.0956-0.01420.00430.1935-0.02590.2192553.947420.5938257.3802
480.0035-0.00280.00340.0057-0.00310.0028-0.0083-0.00550.0005-0.0026-0.01510.01330.00090.0109-0.00150.12920.056-0.00620.1533-0.01380.0867544.6211-15.2435264.1677
490.0001-0.00030.0010.000700.00210.0425-0.0127-0.00940.00160.0120.0080.0020.003-00.33030.0509-0.08090.28060.02820.2514548.7875-35.7923264.1091
500.0046-0.00370.00170.0031-0.00050.00130.01680.001-0.0193-0.0040.001-0.01750.02670.02430.01690.18580.1142-0.09990.13610.05580.1872555.5053-38.2533256.1685
510.0019-0.00270.00080.0031-0.0023-0.00070.0363-0.0095-0.00560.00870.04120.00170.05860.0416-00.22280.1304-0.05690.37120.0120.3597574.1101-30.5186262.5999
520.00010.0001-0.00040.00030.00010.00030.00120.0034-0.0004-0.0063-0.0053-0.0023-0.00310.001-00.7765-0.0240.01940.7411-0.09860.7504541.342325.7076274.355
530.01670.0178-0.0250.0201-0.0280.0388-0.00070.00050.0013-0.0013-0.0008-0.0008-0.00070.00101.32670.011-0.01181.3389-0.0031.3287529.850527.5341277.698
540.00550.00230.00390.00120.00110.0048-0.0020.0018-0.0008-0.0006-0.00160.0008-0.0002-0.000700.80090.00470.02090.7748-0.04930.7836540.201734.689271.9165
55-0.0004-0.00140.00070.00080.00110.0021-0.0027-0.0051-0.0033-0.0023-0.00260.0020.00080.0162-00.22770.0212-0.01780.2512-0.01620.1049543.619412.6054271.9013
560.0015-0.00170.00250.0007-0.00110.001-0.00180.00110.00680.02210.005-0.0011-0.0091-0.009900.33560.08270.00020.3653-0.0130.2783520.03174.2455245.7423
570.0004-0.00010.00120.001600.00220.0210.02170.01480.00760.0172-0.003-0.0011-0.0003-00.27090.0630.07530.3726-0.00850.3162522.80375.4543243.0416
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 946 )
3X-RAY DIFFRACTION3chain 'A' and (resid 947 through 1154 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1155 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 776 )
11X-RAY DIFFRACTION11chain 'B' and (resid 777 through 994 )
12X-RAY DIFFRACTION12chain 'B' and (resid 995 through 1220 )
13X-RAY DIFFRACTION13chain 'C' and (resid 3 through 26 )
14X-RAY DIFFRACTION14chain 'C' and (resid 27 through 51 )
15X-RAY DIFFRACTION15chain 'C' and (resid 52 through 104 )
16X-RAY DIFFRACTION16chain 'C' and (resid 105 through 175 )
17X-RAY DIFFRACTION17chain 'C' and (resid 176 through 209 )
18X-RAY DIFFRACTION18chain 'C' and (resid 210 through 268 )
19X-RAY DIFFRACTION19chain 'E' and (resid 3 through 65 )
20X-RAY DIFFRACTION20chain 'E' and (resid 66 through 82 )
21X-RAY DIFFRACTION21chain 'E' and (resid 83 through 103 )
22X-RAY DIFFRACTION22chain 'E' and (resid 104 through 122 )
23X-RAY DIFFRACTION23chain 'E' and (resid 123 through 215 )
24X-RAY DIFFRACTION24chain 'F' and (resid 72 through 86 )
25X-RAY DIFFRACTION25chain 'F' and (resid 87 through 103 )
26X-RAY DIFFRACTION26chain 'F' and (resid 104 through 116 )
27X-RAY DIFFRACTION27chain 'F' and (resid 117 through 132 )
28X-RAY DIFFRACTION28chain 'F' and (resid 133 through 142 )
29X-RAY DIFFRACTION29chain 'F' and (resid 143 through 147 )
30X-RAY DIFFRACTION30chain 'F' and (resid 148 through 155 )
31X-RAY DIFFRACTION31chain 'H' and (resid 3 through 16 )
32X-RAY DIFFRACTION32chain 'H' and (resid 17 through 30 )
33X-RAY DIFFRACTION33chain 'H' and (resid 31 through 43 )
34X-RAY DIFFRACTION34chain 'H' and (resid 44 through 53 )
35X-RAY DIFFRACTION35chain 'H' and (resid 54 through 82 )
36X-RAY DIFFRACTION36chain 'H' and (resid 83 through 92 )
37X-RAY DIFFRACTION37chain 'H' and (resid 93 through 106 )
38X-RAY DIFFRACTION38chain 'H' and (resid 107 through 118 )
39X-RAY DIFFRACTION39chain 'H' and (resid 119 through 127 )
40X-RAY DIFFRACTION40chain 'H' and (resid 128 through 140 )
41X-RAY DIFFRACTION41chain 'H' and (resid 141 through 146 )
42X-RAY DIFFRACTION42chain 'I' and (resid 2 through 52 )
43X-RAY DIFFRACTION43chain 'I' and (resid 53 through 116 )
44X-RAY DIFFRACTION44chain 'J' and (resid 1 through 14 )
45X-RAY DIFFRACTION45chain 'J' and (resid 15 through 26 )
46X-RAY DIFFRACTION46chain 'J' and (resid 27 through 56 )
47X-RAY DIFFRACTION47chain 'J' and (resid 57 through 65 )
48X-RAY DIFFRACTION48chain 'K' and (resid 1 through 9 )
49X-RAY DIFFRACTION49chain 'K' and (resid 10 through 39 )
50X-RAY DIFFRACTION50chain 'K' and (resid 40 through 82 )
51X-RAY DIFFRACTION51chain 'K' and (resid 83 through 114 )
52X-RAY DIFFRACTION52chain 'L' and (resid 27 through 41 )
53X-RAY DIFFRACTION53chain 'L' and (resid 42 through 46 )
54X-RAY DIFFRACTION54chain 'L' and (resid 47 through 51 )
55X-RAY DIFFRACTION55chain 'L' and (resid 52 through 70 )
56X-RAY DIFFRACTION56chain 'T' and (resid 19 through 29 )
57X-RAY DIFFRACTION57chain 'R' and (resid 1 through 8 )

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