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- PDB-4ifd: Crystal structure of an 11-subunit eukaryotic exosome complex bou... -

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Basic information

Entry
Database: PDB / ID: 4ifd
TitleCrystal structure of an 11-subunit eukaryotic exosome complex bound to RNA
Components
  • (Exosome complex component ...) x 9
  • (Exosome complex exonuclease ...) x 2
  • RNA (45-MER)
KeywordsHYDROLASE/RNA / EXOSOME / RNA / RRP44 / DIS3 / PIN / RRP6 / EXONUCLEASE / ENDONUCLEASE / HYDROLASE / NUCLEASE / RIBONUCLEASE / RNA PROCESSING / HYDROLASE-RNA complex
Function / homology
Function and homology information


nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / mRNA decay by 3' to 5' exoribonuclease / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / nuclear polyadenylation-dependent mRNA catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing / regulatory ncRNA 3'-end processing / U1 snRNA 3'-end processing ...nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / mRNA decay by 3' to 5' exoribonuclease / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / nuclear polyadenylation-dependent mRNA catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing / regulatory ncRNA 3'-end processing / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / exosome (RNase complex) / CUT catabolic process / cytoplasmic exosome (RNase complex) / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / nuclear-transcribed mRNA catabolic process, non-stop decay / nuclear exosome (RNase complex) / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / histone mRNA catabolic process / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / rRNA catabolic process / rRNA primary transcript binding / mRNA 3'-UTR AU-rich region binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA catabolic process / regulation of telomere maintenance / nonfunctional rRNA decay / Major pathway of rRNA processing in the nucleolus and cytosol / rRNA metabolic process / mRNA catabolic process / nuclear-transcribed mRNA catabolic process / RNA processing / RNA endonuclease activity / mRNA processing / manganese ion binding / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / endonuclease activity / tRNA binding / single-stranded RNA binding / nucleotide binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2660 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #880 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #700 / : / Exosome complex component CSL4, N-terminal domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / Exosome complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal domain / Exosome-associated factor Rrp6, N-terminal / Exosome complex exonuclease RRP44, S1 domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2660 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #880 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #700 / : / Exosome complex component CSL4, N-terminal domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / Exosome complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal domain / Exosome-associated factor Rrp6, N-terminal / Exosome complex exonuclease RRP44, S1 domain / Exosome complex exonuclease Rrp6-like / : / PMC2NT (NUC016) domain / S1 domain / PIN domain / Exosome complex component RRP45 / Rrp40, S1 domain / : / Exosome complex component RRP40, S1 domain / Exosome complex component CSL4, C-terminal / Exosome complex component, N-terminal domain / Exosome complex component Csl4 / Exosome component EXOSC1/CSL4 / Exosome complex exonuclease RRP4 N-terminal region / RRP4, S1 domain / Rrp44-like cold shock domain / Rrp44-like cold shock domain / : / KH domain / Exosome complex RNA-binding protein 1/RRP40/RRP4 / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / GHMP Kinase, N-terminal domain / : / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / : / Ribonuclease II/R / RNB domain / RNB / : / K Homology domain, type 1 / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / HRDC domain superfamily / Large family of predicted nucleotide-binding domains / 3'-5' exonuclease / PIN domain / K Homology domain, type 1 / 3'-5' exonuclease / 3'-5' exonuclease domain / Ribosomal Protein S8; Chain: A, domain 1 / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / K Homology domain, type 1 superfamily / PIN-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Ribosomal Protein S5; domain 2 / S1 domain profile. / HRDC-like superfamily / Ribosomal protein S1-like RNA-binding domain / Nucleic acid-binding proteins / S1 domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / Up-down Bundle / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / RNA / RNA (> 10) / Exosome complex component RRP43 / Exosome complex component RRP4 / Exosome complex component SKI6 / Exosome complex component MTR3 / Exosome complex component RRP46 / Exosome complex component CSL4 / Exosome complex component RRP45 ...BROMIDE ION / RNA / RNA (> 10) / Exosome complex component RRP43 / Exosome complex component RRP4 / Exosome complex component SKI6 / Exosome complex component MTR3 / Exosome complex component RRP46 / Exosome complex component CSL4 / Exosome complex component RRP45 / Exosome complex exonuclease DIS3 / Exosome complex component RRP40 / Exosome complex exonuclease RRP6 / Exosome complex component RRP42
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.805 Å
AuthorsMakino, D.L. / Conti, E.
CitationJournal: Nature / Year: 2013
Title: Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex.
Authors: Makino, D.L. / Baumgartner, M. / Conti, E.
History
DepositionDec 14, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2013Group: Database references
Revision 1.2Nov 13, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exosome complex component RRP45
B: Exosome complex component SKI6
C: Exosome complex component RRP43
D: Exosome complex component RRP46
E: Exosome complex component RRP42
F: Exosome complex component MTR3
G: Exosome complex component RRP40
H: Exosome complex component RRP4
I: Exosome complex component CSL4
J: Exosome complex exonuclease DIS3
K: Exosome complex exonuclease RRP6
R: RNA (45-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)438,16230
Polymers436,61812
Non-polymers1,54418
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54990 Å2
ΔGint-266 kcal/mol
Surface area138770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.090, 107.440, 150.460
Angle α, β, γ (deg.)90.00, 110.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Exosome complex component ... , 9 types, 9 molecules ABCDEFGHI

#1: Protein Exosome complex component RRP45 / Ribosomal RNA-processing protein 45


Mass: 33870.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: D9954.1, RRP45, YDR280W / Plasmid: pETMCN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05636
#2: Protein Exosome complex component SKI6 / Extracellular mutant protein 20 / Ribosomal RNA-processing protein 41 / Superkiller protein 6


Mass: 27794.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: ECM20, G7587, RRP41, SKI6, YGR195W / Plasmid: pETMCN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46948
#3: Protein Exosome complex component RRP43 / Ribosomal RNA-processing protein 43


Mass: 43977.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RRP43, YCR035C, YCR35C, YCR522 / Plasmid: pETMCN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P25359
#4: Protein Exosome complex component RRP46 / Ribosomal RNA-processing protein 46


Mass: 26913.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RRP46, YGR095C / Plasmid: pETMCN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P53256
#5: Protein Exosome complex component RRP42 / Ribosomal RNA-processing protein 42


Mass: 29294.398 Da / Num. of mol.: 1 / Mutation: V138I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RRP42, YDL111C / Plasmid: pETMCN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12277
#6: Protein Exosome complex component MTR3 / mRNA transport regulator 3


Mass: 27559.869 Da / Num. of mol.: 1 / Mutation: T75S, M161T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: G6676, MTR3, YGR158C / Plasmid: pETMCN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P48240
#7: Protein Exosome complex component RRP40 / Ribosomal RNA-processing protein 40


Mass: 26778.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RRP40, YOL142W / Plasmid: pETMCN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q08285
#8: Protein Exosome complex component RRP4 / Ribosomal RNA-processing protein 4


Mass: 39714.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RRP4, YHR069C / Plasmid: pECK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38792
#9: Protein Exosome complex component CSL4 / CEP1 synthetic lethal protein 4


Mass: 32805.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CSL4, N1154, SKI4, YNL232W / Plasmid: pETM13 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P53859

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Exosome complex exonuclease ... , 2 types, 2 molecules JK

#10: Protein Exosome complex exonuclease DIS3 / Chromosome disjunction protein 3 / Ribosomal RNA-processing protein 44


Mass: 113983.898 Da / Num. of mol.: 1 / Mutation: D171N, D551N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: DIS3, O2197, RRP44, YOL021C / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q08162, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#11: Protein Exosome complex exonuclease RRP6 / Ribosomal RNA-processing protein 6


Mass: 19876.869 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 518-693
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RRP6, UNC733, YOR001W / Plasmid: pECK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q12149, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters

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RNA chain , 1 types, 1 molecules R

#12: RNA chain RNA (45-MER)


Mass: 14046.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Sequence designed based on biochemical data.

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Non-polymers , 6 types, 262 molecules

#13: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Br
#14: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#15: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#16: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#17: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 10

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.02M Tris pH7.5, 0.05M NaCl, 0.001M MnCl2, 0.002M MgCl2, 1mM TCEP, 0.15M MES pH6.5, 0.27M NaBr, 11.4-12.2% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9199 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9199 Å / Relative weight: 1
ReflectionResolution: 2.805→49.64 Å / Num. all: 99137 / Num. obs: 99137 / % possible obs: 87.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.8 % / Biso Wilson estimate: 59.5 Å2 / Rmerge(I) obs: 0.176 / Net I/σ(I): 12.25
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.8-32.50.5481.8911922156.5
3-3.24.490.4893.5511179169.2
3.2-3.512.990.4716.3517744199.5
3.5-3.816.20.31810.3312650199.9
3.8-4.216.680.2214.1211763199.9
4.2-516.640.1519.0713703199.9
5-616.610.14219.878451199.9
6-816.220.11922.316727199.7
8-2015.830.07432.434677199.7
20-49.6415.760.06935.76321191.2

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NN6, 2WP8, 2JA9, 2JE6

2nn6

2wp8

2ja9

2je6


Resolution: 2.805→49.638 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 24.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 4956 5 %RANDOM
Rwork0.1825 ---
all0.1846 99137 --
obs0.1846 99101 87.86 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.805→49.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25991 540 54 244 26829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00327093
X-RAY DIFFRACTIONf_angle_d0.54236836
X-RAY DIFFRACTIONf_dihedral_angle_d9.90310175
X-RAY DIFFRACTIONf_chiral_restr0.0354351
X-RAY DIFFRACTIONf_plane_restr0.0044662
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.8046-2.83650.3492700.30461336133638
2.8365-2.86980.35811060.29322015201557
2.8698-2.90480.30461220.29382312231264
2.9048-2.94160.34561170.29242233223364
2.9416-2.98030.36341220.28692316231664
2.9803-3.02110.32291170.27872217221763
3.0211-3.06430.33621200.26362287228764
3.0643-3.110.31321190.26022256225664
3.11-3.15860.29241330.25392516251671
3.1586-3.21040.31021630.25243109310987
3.2104-3.26570.2931850.24013510351099
3.2657-3.32510.3091860.23335323532100
3.3251-3.3890.25261860.21935413541100
3.389-3.45820.26141890.214235893589100
3.4582-3.53340.26451870.195935443544100
3.5334-3.61550.22491880.194835743574100
3.6155-3.70590.22921880.185335673567100
3.7059-3.80610.24751860.17635393539100
3.8061-3.9180.20311890.1735853585100
3.918-4.04450.19051870.169835573557100
4.0445-4.18890.21611890.159335893589100
4.1889-4.35660.18911870.150535703570100
4.3566-4.55470.17861880.143235683568100
4.5547-4.79470.17221880.136535763576100
4.7947-5.09480.1761910.143336123612100
5.0948-5.48770.21461870.157735613561100
5.4877-6.03910.23581900.171236003600100
6.0391-6.91090.22341900.181436103610100
6.9109-8.69940.17791900.158436233623100
8.6994-49.64580.1751960.15937013701100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.92940.29130.25291.5279-0.15251.78010.0722-0.1833-0.27610.3481-0.0223-0.2480.22870.11530.04770.56730.09-0.14960.20030.05970.3884141.5112-4.2726205.1851
20.441-0.21490.02320.3590.33370.4692-0.0776-0.17370.10240.35130.0822-0.0766-0.06510.1633-00.626-0.0229-0.10340.287-0.01650.3947139.904142.3845202.7967
30.4703-0.24150.08990.31090.09450.28610.15830.0681-0.1864-0.3683-0.12630.24460.3973-0.1936-00.7377-0.0796-0.02660.87350.01240.5761122.060328.4635121.9292
40.91690.07880.23471.48120.14771.0524-0.13230.4658-0.1995-0.21930.219-0.15960.21570.26610.02050.44320.07660.14651.2502-0.1380.5646161.79019.3733129.7451
50.28010.1174-0.18170.1185-0.00150.1535-0.3637-0.26510.25630.08290.16780.3363-0.2102-0.35530.00010.80650.25030.19671.019-0.12710.860277.28235.5149208.1468
60.025-0.01190.008-0.00050.00040.01750.0574-0.4636-0.02750.4583-0.02-0.0701-0.20340.2008-01.95460.06080.03821.6295-0.00451.4118132.074729.1686222.8311
70.58420.19240.18990.5846-0.01630.6283-0.01340.10680.0110.03160.04980.05970.0418-0.088900.3539-0.01210.0070.31510.00510.3309116.865516.7855173.9893
80.24760.28090.14810.59160.29980.1656-0.05980.33250.273-0.4012-0.0001-0.0677-0.17350.5582-0.05670.5106-0.13330.09481.26640.12160.4452146.857540.4667111.2989
90.0612-0.01530.01470.0338-0.0040.0404-0.0090.14680.1318-0.22230.02320.46880.2068-0.42990.00011.1275-0.08640.08941.8881-0.30120.7299145.798211.02795.2145
100.0095-0.0127-0.01070.00280.00930.00120.11890.18140.02530.2413-0.1109-0.1615-0.08320.178701.8674-0.0001-0.08781.7902-0.13951.9529135.570624.7207143.4691
110.87980.4595-0.08840.60980.13621.0774-0.01740.29730.2703-0.03270.0606-0.0086-0.1460.1904-0.00010.5625-0.13990.02660.79060.19160.5333148.557855.0109139.8855
120.57050.2597-0.16360.87190.02540.3109-0.0892-0.37450.03880.5398-0.0187-0.0772-0.1074-0.2593-00.9328-0.0185-0.01520.6011-0.00610.5565106.7717.444211.4245
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN GG1 - 236
2X-RAY DIFFRACTION2CHAIN H AND (RESID 50:357)H0
3X-RAY DIFFRACTION3CHAIN J AND (RESID 249:399)J0
4X-RAY DIFFRACTION4(CHAIN J AND (RESID 491:910 )) OR (CHAIN R AND (RESSEQ -6:-1))J0
5X-RAY DIFFRACTION5(CHAIN I AND (RESSEQ 1:113)) OR (CHAIN K AND (RESID 532:557 ))I0
6X-RAY DIFFRACTION6CHAIN R AND (RESSEQ -44:-30 )R-44 - -30
7X-RAY DIFFRACTION7CHAIN A OR CHAIN B OR CHAIN C OR CHAIN D OR CHAIN E OR CHAIN F OR (CHAIN H AND RESSEQ 2:17) OR (CHAIN K AND RESSEQ 565:619)A2 - 301
8X-RAY DIFFRACTION7CHAIN A OR CHAIN B OR CHAIN C OR CHAIN D OR CHAIN E OR CHAIN F OR (CHAIN H AND RESSEQ 2:17) OR (CHAIN K AND RESSEQ 565:619)B1 - 242
9X-RAY DIFFRACTION7CHAIN A OR CHAIN B OR CHAIN C OR CHAIN D OR CHAIN E OR CHAIN F OR (CHAIN H AND RESSEQ 2:17) OR (CHAIN K AND RESSEQ 565:619)C7 - 394
10X-RAY DIFFRACTION7CHAIN A OR CHAIN B OR CHAIN C OR CHAIN D OR CHAIN E OR CHAIN F OR (CHAIN H AND RESSEQ 2:17) OR (CHAIN K AND RESSEQ 565:619)D1 - 223
11X-RAY DIFFRACTION7CHAIN A OR CHAIN B OR CHAIN C OR CHAIN D OR CHAIN E OR CHAIN F OR (CHAIN H AND RESSEQ 2:17) OR (CHAIN K AND RESSEQ 565:619)E-1 - 265
12X-RAY DIFFRACTION7CHAIN A OR CHAIN B OR CHAIN C OR CHAIN D OR CHAIN E OR CHAIN F OR (CHAIN H AND RESSEQ 2:17) OR (CHAIN K AND RESSEQ 565:619)F4 - 248
13X-RAY DIFFRACTION7CHAIN A OR CHAIN B OR CHAIN C OR CHAIN D OR CHAIN E OR CHAIN F OR (CHAIN H AND RESSEQ 2:17) OR (CHAIN K AND RESSEQ 565:619)H2 - 17
14X-RAY DIFFRACTION7CHAIN A OR CHAIN B OR CHAIN C OR CHAIN D OR CHAIN E OR CHAIN F OR (CHAIN H AND RESSEQ 2:17) OR (CHAIN K AND RESSEQ 565:619)K565 - 619
15X-RAY DIFFRACTION8CHAIN J AND (RESID 400:490)J0
16X-RAY DIFFRACTION9CHAIN J AND RESID 911:1001J911 - 1001
17X-RAY DIFFRACTION10CHAIN R AND (RESSEQ -15:-7)R-15 - -7
18X-RAY DIFFRACTION11(CHAIN J AND RESID 9:237 )J9 - 237
19X-RAY DIFFRACTION12CHAIN I AND RESID 126:291I126 - 291

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