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- PDB-9pvv: RNA polymerase II elongation complex with dC at +1 site, 8-oxo-GT... -

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Basic information

Entry
Database: PDB / ID: 9pvv
TitleRNA polymerase II elongation complex with dC at +1 site, 8-oxo-GTP bound in A-site.
Components
  • (DNA-directed RNA polymerase II subunit ...) x 5
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • Non-template strand DNA
  • RNA
  • Template strand DNA
KeywordsTRANSCRIPTION / RNA polymerase II / oxidative damage / in vitro transcription / 8-oxoguanine
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 / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening ...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 / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / termination of RNA polymerase II transcription / RNA Polymerase II Pre-transcription Events / termination of RNA polymerase III transcription / RNA-templated transcription / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase III promoter / termination of RNA polymerase I transcription / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / transcription by RNA polymerase III / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Dual incision in TC-NER / RNA polymerase I complex / RNA polymerase III complex / transcription elongation by RNA polymerase I / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / translesion synthesis / transcription-coupled nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / mRNA transcription by RNA polymerase II / ribonucleoside binding / DNA-directed RNA polymerase / cytoplasmic stress granule / DNA-directed RNA polymerase activity / 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
RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 ...RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Zinc finger TFIIS-type signature. / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / 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 Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / 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 / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain
Similarity search - Domain/homology
8-OXO-GUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 ...8-OXO-GUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.48 Å
AuthorsHou, P. / Oh, J. / Wang, D.
Funding support United States, Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM102362 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM147652 United States
National Research Foundation (NRF, Korea)RS-2024-00344054 Korea, Republic Of
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Structural basis of transcription-coupled RNA damage by incorporation of oxidized ribonucleotides.
Authors: Peini Hou / Chanjoo Lee / Jenny Chong / Juntaek Oh / Dong Wang /
Abstract: Oxidative stress induces damage to DNA, RNA, and nucleotide pools. Unlike well-studied DNA damage, the formation of RNA damage and the impact of an oxidized ribonucleotide pool on transcription ...Oxidative stress induces damage to DNA, RNA, and nucleotide pools. Unlike well-studied DNA damage, the formation of RNA damage and the impact of an oxidized ribonucleotide pool on transcription fidelity are poorly understood. Here, we investigate the structural basis of transcription-coupled RNA damage and the effect of 8-oxo-guanosine triphosphate (8-oxo-rGTP) on RNA polymerase II (Pol II) transcription fidelity control steps. We revealed that the incorporation efficiency of 8-oxo-rGTP opposite a dC template is comparable to that of GTP. In contrast, the incorporation efficiency of 8-oxo-rGTP opposite a dA template is ~150-fold more efficient than that of GTP. For the extension step, Pol II extends substantially faster from a 3'-8-oxo-rG:dC base pair than from a 3'-8-oxo-rG:dA base pair. For the proofreading step, strikingly, Pol II EC with 3'-8-oxo-rG:dA base pair is much more resistant to backtracking and proofreading than Pol II EC with 3'-8-oxo-rG:dC base pair. Using X-ray crystallography, we revealed that 8-oxo-rGTP adopts different prechemistry binding sites depending on whether it is paired with a dC or a dA template. Upon incorporation, the nucleobase of 8-oxo-rG flips to the -conformation to form a Hoogsteen pair with a dA template, whereas it remains in the -conformation to form a Watson-Crick pair with a dC template. Collectively, our work demonstrates that nucleotide-pool oxidation can directly affect Pol II fidelity control steps and elongation dynamics and induce RNA damage in a transcription-coupled manner.
History
DepositionAug 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: RNA
T: Template strand DNA
N: Non-template strand DNA
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)488,03524
Polymers486,92413
Non-polymers1,11111
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.518, 222.702, 191.185
Angle α, β, γ (deg.)90.00, 97.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

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RNA chain , 1 types, 1 molecules R

#1: RNA chain RNA


Mass: 2934.831 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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DNA chain , 2 types, 2 molecules TN

#2: DNA chain Template strand DNA


Mass: 8699.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain Non-template strand DNA


Mass: 5663.694 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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DNA-directed RNA polymerase II subunit ... , 5 types, 5 molecules ABCIK

#4: 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 S288C (yeast) / Gene: RPO21, RPB1, RPB220, SUA8, YDL140C, D2150 / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P04050, DNA-directed RNA polymerase
#5: 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 S288C (yeast) / Gene: RPB2, RPB150, RPO22, YOR151C / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P08518, DNA-directed RNA polymerase
#6: 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 S288C (yeast) / Gene: RPB3, YIL021W / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P16370
#10: 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 S288C (yeast) / Gene: RPB9, YGL070C / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P27999
#12: 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 S288C (yeast) / Gene: RPB11, YOL005C / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P38902

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DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL

#7: 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 S288C (yeast) / Gene: RPB5, RPA7, RPC9, YBR154C, YBR1204 / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P20434
#8: 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 S288C (yeast) / Gene: RPO26, RPB6, YPR187W, P9677.8 / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P20435
#9: 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 S288C (yeast) / Gene: RPB8, YOR224C, YOR50-14 / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P20436
#11: 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 S288C (yeast) / Gene: RPB10, YOR210W / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P22139
#13: 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 S288C (yeast) / Gene: RPC10, RPB12, YHR143W-A, YHR143BW / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P40422

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Non-polymers , 3 types, 11 molecules

#14: Chemical ChemComp-8GT / 8-OXO-GUANOSINE-5'-TRIPHOSPHATE


Mass: 539.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O15P3 / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#16: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.45 Å3/Da / Density % sol: 64.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 5mM dioxane, 5mM DTT, 10-12% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.48→39.81 Å / Num. obs: 83763 / % possible obs: 99.1 % / Redundancy: 7.2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.298 / Rpim(I) all: 0.118 / Rrim(I) all: 0.321 / Χ2: 0.91 / Net I/σ(I): 5.5 / Num. measured all: 605364
Reflection shellResolution: 3.48→3.55 Å / % possible obs: 99.8 % / Redundancy: 7.5 % / Rmerge(I) obs: 2.215 / Num. measured all: 34168 / Num. unique obs: 4573 / CC1/2: 0.709 / Rpim(I) all: 0.864 / Rrim(I) all: 2.38 / Χ2: 0.93 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
Aimlessdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.48→38.52 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2582 1993 2.39 %
Rwork0.2178 --
obs0.2188 83424 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.48→38.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28073 986 43 0 29102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00429728
X-RAY DIFFRACTIONf_angle_d0.68240381
X-RAY DIFFRACTIONf_dihedral_angle_d17.96311349
X-RAY DIFFRACTIONf_chiral_restr0.0424553
X-RAY DIFFRACTIONf_plane_restr0.0055054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.48-3.570.38151400.33865723X-RAY DIFFRACTION98
3.57-3.660.34731430.30365817X-RAY DIFFRACTION99
3.66-3.770.3151430.28075837X-RAY DIFFRACTION99
3.77-3.890.30141430.25845839X-RAY DIFFRACTION99
3.89-4.030.27031430.24115820X-RAY DIFFRACTION99
4.03-4.190.25531430.21775859X-RAY DIFFRACTION99
4.19-4.380.24081420.20315778X-RAY DIFFRACTION99
4.38-4.610.20971400.19375782X-RAY DIFFRACTION98
4.61-4.90.21821390.19285660X-RAY DIFFRACTION96
4.9-5.280.29091440.20595879X-RAY DIFFRACTION100
5.28-5.810.29191410.22375841X-RAY DIFFRACTION100
5.81-6.650.28171460.23095908X-RAY DIFFRACTION100
6.65-8.360.24431430.20545841X-RAY DIFFRACTION99
8.36-38.520.2051430.17295847X-RAY DIFFRACTION98
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)
10.29290.1280.58692.6746-0.10811.28720.02960.1805-0.21790.1089-0.3573-0.50160.40160.59380.11131.1028-0.188-0.12210.88960.10270.807913.902614.046538.9486
20.7077-0.4480.52150.2906-0.2890.3532-0.2557-0.3186-0.10790.4083-0.1-0.82380.22590.29790.07412.1274-0.0917-0.32662.2098-0.07392.546251.984312.53974.9879
30.8186-0.1964-0.36221.4941-0.36980.59920.3386-0.15040.2498-0.4186-0.1414-0.4705-0.37470.4433-0.0121.2373-0.3167-0.18910.8310.05050.963320.851812.099442.6998
40.83450.60961.00540.47450.5981.6638-0.1799-0.69040.83040.0939-0.86510.4052-0.33010.95060.37311.2464-0.5227-0.00682.4819-0.0262.15446.578912.494671.6071
50.4695-0.15440.21520.5191-0.07281.01310.0706-0.02180.10580.2-0.0809-0.23840.13060.39480.04330.9553-0.1379-0.18990.56580.1340.598220.4861-2.989645.4765
60.43180.02880.32710.74290.03631.1378-0.0464-0.11120.10920.40350.0946-0.04170.12880.23030.02711.6477-0.0478-0.41210.71980.19880.824125.6288-16.364374.3165
70.87810.3726-0.17040.2669-0.72570.8990.02480.04490.49750.0792-0.00630.1659-0.31930.0841-0.01671.5945-0.259-0.09280.50470.03630.70781.360742.850939.6905
81.94750.89450.48240.66030.51861.05230.1445-0.01870.07240.16170.0743-0.20130.22690.1369-0.18171.4412-0.2209-0.07660.6403-0.11850.785426.386937.462474.4807
90.24170.35060.21760.4608-0.06180.8106-0.09970.10040.0222-0.26530.0746-0.17970.15730.25320.08491.3188-0.2121-0.06710.48950.00620.601811.185634.047747.2989
101.47390.6091-0.22051.46440.36570.79010.1801-0.33260.19840.1773-0.15830.0804-0.3138-0.152-0.07981.45510.0306-0.12140.4969-0.05650.5284-6.888835.988470.9564
110.4996-0.03340.11530.75070.19760.847-0.07820.14220.00310.03030.0331-0.0858-0.43710.19420.07620.7748-0.17660.01040.46480.02050.4429-7.258310.269632.9364
120.8785-0.16280.65810.3351-0.11290.6046-0.10270.22460.03650.0534-0.1419-0.26140.14280.47720.12490.9572-0.1072-0.12350.81080.2890.7125.1686-3.593730.7062
132.75090.1826-0.70621.8405-0.47020.8598-0.2018-0.0675-0.0962-0.0169-0.00180.2683-0.04380.2093-0.1010.0007-0.53940.31020.9098-0.06460.5992-43.2474-16.175831.1337
140.3003-0.1793-0.16730.46530.89222.10610.0432-0.1847-0.1208-0.366-0.2124-0.2158-0.78680.1423-0.1650.043-0.22880.02380.76320.06740.4373-23.20941.066920.791
151.0627-1.1962-1.25531.33641.28872.6746-0.0168-0.0418-0.27760.1815-0.28540.58280.4570.43520.04430.9004-0.1824-0.08340.67070.0350.5684-26.7017-4.50317.3553
161.34970.35140.21461.8616-0.24511.01440.11110.51960.0966-0.31150.0880.4288-0.2912-0.2339-0.19980.52960.0538-0.01050.56270.020.4022-28.92510.900415.5287
171.04520.8287-0.13910.97650.22830.3667-0.0092-0.05780.12550.6809-0.02070.2943-0.2229-0.48120.01381.2388-0.24280.0110.79320.03170.8121-34.1979-14.243350.7991
181.29610.15740.34651.749-0.24111.08680.16730.0883-0.08750.07860.00020.20160.5907-0.3273-0.011.15-0.2138-0.1780.74590.00530.6832-33.313-21.218629.5374
191.47040.3299-0.35220.5814-0.22422.4170.00790.0242-0.18920.2017-0.10290.29930.72390.525-0.02361.1402-0.2003-0.56751.27190.26811.177245.9032-20.710393.2431
200.250.2719-0.00160.45120.17190.0554-0.21510.0383-0.07140.76050.5948-0.0231-0.41210.5676-0.16581.60070.3373-0.44422.458-0.00061.45957.2595-17.752991.8144
212.68931.8327-1.36461.3084-1.01511.03580.323-0.17680.39580.03460.1354-0.1075-0.32930.4725-0.15031.2655-0.0495-0.37761.3909-0.15320.991856.8293-10.373983.7441
220.80020.09760.09430.92980.78551.96440.11770.17560.1224-0.2169-0.2854-0.2453-0.28750.1540.09471.6390.013-0.55781.05860.16911.037643.4966-22.627968.1859
232.5358-0.05920.36570.03060.01220.0996-0.05490.16080.1994-0.48490.2479-0.2458-0.17320.2990.08121.50480.2557-0.59491.46780.39162.17651.8833-31.035139.0042
247.89161.9946-1.52391.57930.14224.1958-0.0680.224-0.8101-0.20830.1593-0.6480.74390.61170.00761.09950.262-0.10021.03560.03881.062739.4232-38.821344.0252
251.67120.1572-0.05930.49840.84642.3624-0.17160.0772-0.27570.1866-0.1965-0.36960.4890.24810.04550.96670.0445-0.12640.78240.28210.773726.1984-29.206532.6787
261.18710.35780.6243.21171.09360.6058-0.27750.1915-0.16620.0195-0.22940.0570.1592-0.0540.02751.77470.0582-0.15340.94630.00451.083920.4339-34.961719.5826
273.8486-2.70143.04671.9262-2.35793.99730.0277-0.1928-0.7139-0.05260.02070.28870.4991-0.1532-0.09731.25120.42050.18411.14620.20151.006419.8079-35.049927.6518
282.8655-1.1212-1.30032.3278-0.89441.80450.0729-0.226-0.56290.2708-0.13560.21750.4849-0.30830.04381.26560.04940.0941.56010.22341.028829.1375-38.046828.8261
294.5348-2.0149-3.85253.62050.37754.0402-0.09740.23010.1434-0.37320.0175-0.4538-0.36240.56260.01381.14970.0580.26991.12580.08370.983838.0058-30.530537.7174
300.3671-0.3201-0.40642.49940.61450.4722-0.03480.2713-0.5453-0.0191-0.12460.0102-0.30750.2774-0.03191.24920.0080.13081.34940.13371.054840.9739-31.620341.9447
313.96650.86153.66563.9805-3.90789.2255-0.09380.2703-0.317-0.0545-0.28440.13220.30380.29680.15221.8221-0.0236-0.09780.93030.2711.12228.1135-39.171738.2359
322.14310.8410.07961.6705-1.13461.0850.3551-0.4097-0.06480.26610.16950.3053-0.098-0.0463-0.01081.5767-0.07510.44711.00670.61091.2959-24.3987-48.047466.1872
331.6033-1.36220.82195.10560.46960.8279-0.2757-0.120.11030.2606-0.09070.1546-0.093-0.0746-0.08531.675-0.4475-0.00481.28570.11781.0969-22.5543-33.181465.9863
341.2661-0.4540.17861.0263-0.75732.54010.2141-0.7868-0.27040.28140.2632-0.0253-0.0504-0.6995-0.1931.3543-0.45350.06420.90360.22631.0951-26.1566-42.280567.3235
350.33220.63230.29562.1541-1.90316.06040.16060.2823-0.8112-0.5765-0.1556-0.06940.36240.24110.01841.6168-0.3378-0.11030.86820.14471.0361-22.1789-48.272550.0005
362.9786-0.5155-2.20563.361-2.80424.73760.17350.64210.0915-0.7023-0.11560.38160.1755-0.6213-0.09281.652-0.7926-0.17230.68990.281.8026-30.6283-50.396843.9545
372.44920.97051.31861.70981.24743.1453-0.0362-0.1843-0.70520.1964-0.0960.3325-0.05680.0191-0.14611.5561-0.308-0.03610.6640.27190.9588-17.0044-45.225258.7895
381.9054-1.61321.34676.679-5.67825.14890.0109-0.263-0.22780.38680.1994-0.33410.42220.24210.04011.6004-0.491-0.05370.59870.35420.9334-10.9706-48.525268.5371
391.58980.01790.13851.63420.43810.12670.1228-0.0612-0.40530.33570.20220.02180.1087-0.0937-0.06181.2924-0.4046-0.01770.64850.16340.7921-15.4901-42.408964.9449
400.07670.08570.07640.56580.65630.85530.17020.48830.8434-0.58760.025-0.4026-1.17880.4967-0.17252.0981-0.2367-0.46691.5780.76781.5361-14.4051-57.030867.7797
412.8496-2.24590.68151.8426-0.55020.3509-0.09190.7521-0.0556-0.8712-0.4012-0.34020.57510.85620.24231.6972-0.30.01560.85610.32561.0545-10.8271-51.461656.2674
428.3725-1.2179-3.53435.41361.83767.5707-0.1344-0.17970.11410.3002-0.32980.46950.0392-0.37040.06311.2996-0.32630.04050.69290.2261.0782-27.2309-47.027758.443
434.10340.1304-0.80862.6397-1.89295.1480.1220.00010.057-0.01510.5334-0.180.0406-0.20770.0051.5753-0.0216-0.33051.3231-0.31780.794830.368644.884496.9785
443.45030.58861.02114.3371.35941.89040.215-0.1555-0.75230.3744-0.0212-0.52820.29620.09180.03041.4471-0.1642-0.21480.8085-0.04770.839737.226341.2148105.5221
452.13320.38051.18170.0650.20140.64570.18720.3568-0.48560.0364-0.21060.215-0.0633-0.04560.01651.66240.0844-0.36561.4247-0.19291.354513.956328.571393.9154
460.90170.6959-0.15080.67430.2277.6207-0.0932-0.8240.1420.1553-0.15510.8296-0.1375-0.45370.03491.5509-0.22520.17811.2558-0.04460.4336-5.021825.502393.0563
478.07610.273-5.40050.0059-0.18473.6014-0.20490.1417-0.5097-0.17180.0703-0.38670.290.27360.1421.7074-0.26650.1011.24080.2561.273212.676418.190487.3701
483.65281.6352-0.24896.11212.47257.66740.2551-0.7181-0.24770.52390.1140.1778-0.0638-0.47030.02931.80190.0622-0.04741.5672-0.16090.7521-0.021726.690996.3346
491.4879-1.3819-0.53016.3658-2.48592.34370.0726-0.39940.41260.2893-0.27110.4662-0.1426-0.44330.18681.6946-0.0384-0.32631.667-0.07741.94946.121717.1036101.7662
500.5394-0.5314-0.20490.55630.30050.32580.1013-0.22870.1508-0.0566-0.0264-0.249-0.18680.1088-0.4247-0.4716-0.36360.32880.47030.24450.209-24.34167.607429.9324
510.315-0.81041.22424.0258-3.41344.7944-0.32220.24910.2779-0.1527-0.3324-0.0591-0.1302-0.2313-0.00280.34010.22940.08310.6688-0.0910.7073-31.49877.061428.7873
522.31211.410.40110.91350.04750.82350.04920.03910.54410.00330.03050.1721-0.1463-0.39350.0366-0.185-0.04980.51470.6582-0.14191.0986-34.888318.43734.0374
531.65690.55530.0941.4480.41172.72450.0392-0.0605-0.09150.1406-0.13790.5704-0.69880.0556-0.4107-0.0697-0.01260.18710.5794-0.08050.5266-29.01615.795235.5982
540.52310.70180.23842.93270.67680.18510.0910.1605-0.38760.2826-0.2785-0.99260.01290.01890.12021.3152-0.1541-0.1310.6732-0.00520.7669-11.3666-23.06120.1852
550.7304-0.5297-0.08330.3206-0.02651.03070.30610.2796-0.53910.00750.04860.07240.50960.1222-0.11581.006-0.1158-0.21210.57930.01250.5826-19.2706-27.736428.3733
563.72422.50420.81236.14140.02490.36540.3951-0.0544-0.6528-0.03940.3616-0.29330.19160.2026-0.08461.5653-0.5053-0.13380.6102-0.16360.5793-18.2416-36.879626.6904
570.9919-0.8164-0.0240.72050.10220.32880.0938-0.078-0.56490.0479-0.0713-0.08190.0853-0.41150.0435-0.2681-0.7343-0.37680.6914-0.13570.7471-38.5298-23.552423.3351
580.66540.32290.2510.27660.20940.2571-0.2363-0.9110.870.7583-0.00750.5015-0.3987-0.3164-0.00922.2484-0.1424-0.10011.82520.11351.5572-7.282233.11019.7677
590.5813-0.1523-1.41980.0480.39423.51990.08850.59790.248-0.4140.1071-0.1341-0.21690.16550.08091.47940.09060.01462.08070.54861.70451.743432.92562.4575
605.5792-0.37514.61776.0192-2.63164.7182-0.1613-0.22530.11090.14270.18170.6026-0.6082-1.0473-0.0132.42430.0509-0.1492.07720.17222.1295-2.512839.920510.6115
614.32854.12294.39175.24536.45598.4704-0.4209-0.42210.58370.3259-0.41850.1891-0.1420.12940.2451.4750.0661-0.26250.74440.03740.7395-5.324.95099.6797
621.83262.5647-1.06583.583-1.48520.6231-0.2737-0.0657-0.4637-0.5847-0.0328-0.18560.33240.18080.15871.3847-0.079-0.10811.0314-0.03870.6347-14.06196.827912.9444
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'R' and (resid 1 through 9 )
2X-RAY DIFFRACTION2chain 'T' and (resid 4 through 13 )
3X-RAY DIFFRACTION3chain 'T' and (resid 14 through 28 )
4X-RAY DIFFRACTION4chain 'N' and (resid 2 through 15 )
5X-RAY DIFFRACTION5chain 'A' and (resid 3 through 845 )
6X-RAY DIFFRACTION6chain 'A' and (resid 846 through 1446 )
7X-RAY DIFFRACTION7chain 'B' and (resid 20 through 212 )
8X-RAY DIFFRACTION8chain 'B' and (resid 213 through 408 )
9X-RAY DIFFRACTION9chain 'B' and (resid 409 through 560 )
10X-RAY DIFFRACTION10chain 'B' and (resid 561 through 750 )
11X-RAY DIFFRACTION11chain 'B' and (resid 751 through 1072 )
12X-RAY DIFFRACTION12chain 'B' and (resid 1073 through 1221 )
13X-RAY DIFFRACTION13chain 'C' and (resid 2 through 26 )
14X-RAY DIFFRACTION14chain 'C' and (resid 27 through 69 )
15X-RAY DIFFRACTION15chain 'C' and (resid 70 through 96 )
16X-RAY DIFFRACTION16chain 'C' and (resid 97 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 4 through 38 )
20X-RAY DIFFRACTION20chain 'E' and (resid 39 through 103 )
21X-RAY DIFFRACTION21chain 'E' and (resid 104 through 141 )
22X-RAY DIFFRACTION22chain 'E' and (resid 142 through 215 )
23X-RAY DIFFRACTION23chain 'F' and (resid 69 through 73 )
24X-RAY DIFFRACTION24chain 'F' and (resid 74 through 83 )
25X-RAY DIFFRACTION25chain 'F' and (resid 84 through 102 )
26X-RAY DIFFRACTION26chain 'F' and (resid 103 through 116 )
27X-RAY DIFFRACTION27chain 'F' and (resid 117 through 127 )
28X-RAY DIFFRACTION28chain 'F' and (resid 128 through 132 )
29X-RAY DIFFRACTION29chain 'F' and (resid 133 through 137 )
30X-RAY DIFFRACTION30chain 'F' and (resid 138 through 147 )
31X-RAY DIFFRACTION31chain 'F' and (resid 148 through 154 )
32X-RAY DIFFRACTION32chain 'H' and (resid 2 through 16 )
33X-RAY DIFFRACTION33chain 'H' and (resid 17 through 30 )
34X-RAY DIFFRACTION34chain 'H' and (resid 31 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 105 )
38X-RAY DIFFRACTION38chain 'H' and (resid 106 through 118 )
39X-RAY DIFFRACTION39chain 'H' and (resid 119 through 126 )
40X-RAY DIFFRACTION40chain 'H' and (resid 127 through 133 )
41X-RAY DIFFRACTION41chain 'H' and (resid 134 through 140 )
42X-RAY DIFFRACTION42chain 'H' and (resid 141 through 146 )
43X-RAY DIFFRACTION43chain 'I' and (resid 2 through 13 )
44X-RAY DIFFRACTION44chain 'I' and (resid 14 through 42 )
45X-RAY DIFFRACTION45chain 'I' and (resid 43 through 64 )
46X-RAY DIFFRACTION46chain 'I' and (resid 65 through 87 )
47X-RAY DIFFRACTION47chain 'I' and (resid 88 through 98 )
48X-RAY DIFFRACTION48chain 'I' and (resid 99 through 111 )
49X-RAY DIFFRACTION49chain 'I' and (resid 112 through 119 )
50X-RAY DIFFRACTION50chain 'J' and (resid 1 through 10 )
51X-RAY DIFFRACTION51chain 'J' and (resid 11 through 16 )
52X-RAY DIFFRACTION52chain 'J' and (resid 17 through 26 )
53X-RAY DIFFRACTION53chain 'J' and (resid 27 through 65 )
54X-RAY DIFFRACTION54chain 'K' and (resid 1 through 30 )
55X-RAY DIFFRACTION55chain 'K' and (resid 31 through 69 )
56X-RAY DIFFRACTION56chain 'K' and (resid 70 through 82 )
57X-RAY DIFFRACTION57chain 'K' and (resid 83 through 114 )
58X-RAY DIFFRACTION58chain 'L' and (resid 28 through 38 )
59X-RAY DIFFRACTION59chain 'L' and (resid 39 through 43 )
60X-RAY DIFFRACTION60chain 'L' and (resid 44 through 53 )
61X-RAY DIFFRACTION61chain 'L' and (resid 54 through 63 )
62X-RAY DIFFRACTION62chain 'L' and (resid 64 through 70 )

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