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- PDB-6drd: RNA Pol II(G) -

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Entry
Database: PDB / ID: 6drd
TitleRNA Pol II(G)
Components
  • (DNA-directed RNA polymerase II subunit ...Polymerase) x 8
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 5
KeywordsTRANSFERASE / RNA Pol II(G) / Gdown1 / transcription repression / molecular mechanism
Function / homology
Function and homology information


HIV elongation arrest and recovery / Formation of the HIV-1 Early Elongation Complex / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / Formation of HIV-1 elongation complex containing HIV-1 Tat / Pausing and recovery of Tat-mediated HIV elongation / Abortive elongation of HIV-1 transcript in the absence of Tat / Tat-mediated HIV elongation arrest and recovery ...HIV elongation arrest and recovery / Formation of the HIV-1 Early Elongation Complex / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / Formation of HIV-1 elongation complex containing HIV-1 Tat / Pausing and recovery of Tat-mediated HIV elongation / Abortive elongation of HIV-1 transcript in the absence of Tat / Tat-mediated HIV elongation arrest and recovery / Tat-mediated elongation of the HIV-1 transcript / Pausing and recovery of HIV elongation / Formation of the Early Elongation Complex / Viral Messenger RNA Synthesis / Cytosolic sensors of pathogen-associated DNA / MicroRNA (miRNA) biogenesis / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / Transcriptional regulation by small RNAs / PIWI-interacting RNA (piRNA) biogenesis / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RNA Polymerase II Pre-transcription Events / Formation of TC-NER Pre-Incision Complex / Formation of HIV elongation complex in the absence of HIV Tat / Formation of RNA Pol II elongation complex / Dual incision in TC-NER / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / Gap-filling DNA repair synthesis and ligation in TC-NER / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Major Pathway / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase II Promoter Escape / RNA Polymerase III Chain Elongation / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Termination / RNA Polymerase III Abortive And Retractive Initiation / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Signaling by FGFR2 IIIa TM / Estrogen-dependent gene expression / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / maintenance of ER location / RNA polymerase II, holoenzyme / regulation of transcription by RNA polymerase I / transcription initiation from RNA polymerase I promoter / nuclear-transcribed mRNA catabolic process, exonucleolytic / transcription elongation from RNA polymerase I promoter / termination of RNA polymerase I transcription / positive regulation of viral transcription / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / LRR domain binding / snRNA transcription by RNA polymerase II / positive regulation of gene expression, epigenetic / mRNA export from nucleus in response to heat stress / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / RNA polymerase II activity / RNA metabolic process / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of translational initiation / somatic stem cell population maintenance / mRNA cleavage / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase II, core complex / transcription by RNA polymerase III / 7-methylguanosine mRNA capping / translation initiation factor binding / transcription elongation from RNA polymerase II promoter / positive regulation of type I interferon production / ribonucleoside binding / DNA-templated transcription, termination / promoter-specific chromatin binding / positive regulation of RNA splicing / DNA-directed 5'-3' RNA polymerase activity / regulation of gene silencing by miRNA / ec:2.7.7.6: / single-stranded RNA binding / fibroblast growth factor receptor signaling pathway / P-body / fibrillar center / microtubule cytoskeleton / mRNA splicing, via spliceosome / transcription-coupled nucleotide-excision repair / single-stranded DNA binding / nuclear envelope / protein-DNA complex / transcription by RNA polymerase II / ec:2.7.7.48:
DNA-directed RNA polymerase, subunit RPB6 / S1 RNA binding domain / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase RBP11 / RNA polymerase Rpb1, funnel domain superfamily / Rpb4/RPC9 superfamily / RNA polymerase Rpb1, domain 7 superfamily / DNA-directed RNA polymerase subunit Rpb5-like / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb1, domain 3 superfamily ...DNA-directed RNA polymerase, subunit RPB6 / S1 RNA binding domain / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase RBP11 / RNA polymerase Rpb1, funnel domain superfamily / Rpb4/RPC9 superfamily / RNA polymerase Rpb1, domain 7 superfamily / DNA-directed RNA polymerase subunit Rpb5-like / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb2, domain 6 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb3/RpoA insert domain / Transcription factor S-II (TFIIS) / RNA polymerase Rpb5, C-terminal domain / RNA polymerase Rpb6 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases N / 8 kDa subunit / RNA polymerases M/15 Kd subunit / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase Rpb8 / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb5, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase, subunit H/Rpb5, conserved site / HRDC-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase subunit, RPB6/omega / Nucleic acid-binding, OB-fold / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / RNA polymerase Rpb2, OB-fold / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain superfamily / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases, subunit N, zinc binding site / RNA-binding domain, S1 / RNA polymerase subunit RPB10 / DNA-directed RNA polymerase II subunit GRINL1 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Pol II subunit B9, C-terminal zinc ribbon / RPB5-like RNA polymerase subunit superfamily / RPB6/omega subunit-like superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb4 / RNA polymerase Rpb2, domain 7 / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb3/Rpb11 dimerisation domain / Zinc finger TFIIS-type profile. / Putative GRINL1B complex locus protein 2 / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerases D / 30 to 40 Kd subunits signature. / Zinc finger TFIIS-type signature. / RNA polymerases M / 15 Kd subunits signature. / RNA polymerases H / 23 Kd subunits signature. / RNA polymerases K / 14 to 18 Kd subunits signature. / RNA polymerases N / 8 Kd subunits signature. / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase II, heptapeptide repeat, eukaryotic / DNA-directed RNA polymerase, subunit N/Rpb10 / RNA polymerase, alpha subunit / RNA polymerase, subunit omega/K/RPB6 / RNA polymerase subunit RPB4/RPC9 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb2, domain 7 / RNA polymerase, beta subunit, conserved site / Archaeal RpoK/eukaryotic RPB6 RNA polymerase subunit / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb4/RPC9, core / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / RNA polymerase, Rpb5, N-terminal / RNA polymerase, Rpb8 / RNA polymerase Rpb1, domain 6
DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB3 ...DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit GRINL1A / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC5
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsYu, X. / Jishage, M. / Shi, Y. / Ganesan, S. / Sali, A. / Chait, B.T. / Asturias, F. / Roeder, R.G.
Funding supportUnited States , 1件
OrganizationGrant numberCountry
National Institutes of Health/National Cancer InstituteR01 CA202245United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1.
Authors: Miki Jishage / Xiaodi Yu / Yi Shi / Sai J Ganesan / Wei-Yi Chen / Andrej Sali / Brian T Chait / Francisco J Asturias / Robert G Roeder /
Abstract: Tight binding of Gdown1 represses RNA polymerase II (Pol II) function in a manner that is reversed by Mediator, but the structural basis of these processes is unclear. Although Gdown1 is ...Tight binding of Gdown1 represses RNA polymerase II (Pol II) function in a manner that is reversed by Mediator, but the structural basis of these processes is unclear. Although Gdown1 is intrinsically disordered, its Pol II interacting domains were localized and shown to occlude transcription factor IIF (TFIIF) and transcription factor IIB (TFIIB) binding by perfect positioning on their Pol II interaction sites. Robust binding of Gdown1 to Pol II is established by cooperative interactions of a strong Pol II binding region and two weaker binding modulatory regions, thus providing a mechanism both for tight Pol II binding and transcription inhibition and for its reversal. In support of a physiological function for Gdown1 in transcription repression, Gdown1 co-localizes with Pol II in transcriptionally silent nuclei of early Drosophila embryos but re-localizes to the cytoplasm during zygotic genome activation. Our study reveals a self-inactivation through Gdown1 binding as a unique mode of repression in Pol II function.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 11, 2018 / Release: Jun 12, 2019
RevisionDateData content typeProviderType
1.0Jun 12, 2019Structure modelrepositoryInitial release

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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
D: DNA-directed RNA polymerase II subunit RPB4
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
G: DNA-directed RNA polymerase II subunit RPB7
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-a
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
M: DNA-directed RNA polymerase II subunit GRINL1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)523,56718
Polymers523,24013
Non-polymers3275
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area51310 Å2
ΔGint-313 kcal/mol
Surface area147180 Å2

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Components

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DNA-directed RNA polymerase II subunit ... , 8 types, 8 molecules ABCDGIKM

#1: Protein/peptide DNA-directed RNA polymerase II subunit RPB1 / Polymerase / RNA polymerase II subunit B1 / DNA-directed RNA polymerase II subunit A / DNA-directed RNA polymerase III largest subunit / RNA-directed RNA polymerase II subunit RPB1


Mass: 217450.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P24928, EC: 2.7.7.6, EC: 2.7.7.48
#2: Protein/peptide DNA-directed RNA polymerase II subunit RPB2 / Polymerase / DNA-directed RNA polymerase II 140 kDa polypeptide / DNA-directed RNA polymerase II subunit B / RNA polymerase II subunit 2 / RNA polymerase II subunit B2


Mass: 134071.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P30876, EC: 2.7.7.6
#3: Protein/peptide DNA-directed RNA polymerase II subunit RPB3 / Polymerase / RNA polymerase II subunit B3 / DNA-directed RNA polymerase II 33 kDa polypeptide / RPB33 / DNA-directed RNA polymerase II subunit C / RPB31


Mass: 31478.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P19387
#4: Protein/peptide DNA-directed RNA polymerase II subunit RPB4 / Polymerase / RNA polymerase II subunit B4 / DNA-directed RNA polymerase II subunit D / RNA polymerase II 16 kDa subunit / RPB16


Mass: 16331.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15514
#7: Protein/peptide DNA-directed RNA polymerase II subunit RPB7 / Polymerase / RNA polymerase II subunit B7 / DNA-directed RNA polymerase II subunit G / RNA polymerase II 19 kDa subunit / RPB19


Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62487
#9: Protein/peptide DNA-directed RNA polymerase II subunit RPB9 / Polymerase / RNA polymerase II subunit B9 / DNA-directed RNA polymerase II subunit I / RNA polymerase II 14.5 kDa subunit / RPB14.5


Mass: 14541.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36954
#11: Protein/peptide DNA-directed RNA polymerase II subunit RPB11-a / Polymerase / RPB11a / DNA-directed RNA polymerase II subunit J-1 / RNA polymerase II 13.3 kDa subunit


Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P52435
#13: Protein/peptide DNA-directed RNA polymerase II subunit GRINL1A / Polymerase / DNA-directed RNA polymerase II subunit M / Glutamate receptor-like protein 1A


Mass: 5756.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P0CAP2

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

#5: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase / RNA polymerases I / II / and III subunit ABC1 / DNA-directed RNA polymerase II 23 kDa polypeptide / DNA-directed RNA polymerase II subunit E / RPB5 homolog / XAP4


Mass: 24659.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P19388
#6: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerase / RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerase II subunit F / DNA-directed RNA polymerases I / and III 14.4 kDa polypeptide / RPABC14.4 / RPB14.4 / RPB6 homolog / RPC15


Mass: 14491.026 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61218
#8: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase / RNA polymerases I / II / and III subunit ABC3 / DNA-directed RNA polymerase II subunit H / DNA-directed RNA polymerases I / and III 17.1 kDa polypeptide / RPB17 / RPB8 homolog / hRPB8


Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P52434
#10: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerase / RNA polymerases I / II / and III subunit ABC5 / DNA-directed RNA polymerase III subunit L / RNA polymerase II 7.6 kDa subunit / RPB7.6 / RPB10 homolog


Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62875
#12: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha / DNA-directed RNA polymerase II subunit K / RNA polymerase II 7.0 kDa subunit / RPB7.0 / RPB10alpha


Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P53803

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Non-polymers , 1 types, 5 molecules

#14: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Zinc

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: hPolII_Gdown1 / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / C2 aperture diameter: 100 µns
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: dev_2666: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 141619 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Refine LS restraints

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.0127194
f_angle_d1.1136743
f_dihedral_angle_d6.13516644
f_chiral_restr0.0644148
f_plane_restr0.0074742

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