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- PDB-6bm4: Pol II elongation complex with an abasic lesion at i-1 position,s... -

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Basic information

Entry
Database: PDB / ID: 6bm4
TitlePol II elongation complex with an abasic lesion at i-1 position,soaking UMPNPP
Components
  • (DNA-directed RNA polymerase II subunit ...) x 5
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • DNA (5'-D(P*CP*AP*(3DR)P*CP*TP*CP*TP*TP*GP*AP*TP*G)-3')
  • RNA (5'-R(*AP*UP*CP*AP*AP*GP*AP*GP*A)-3')
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 / RNA polymerase II transcribes snRNA genes / termination of RNA polymerase II transcription / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape ...RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / termination of RNA polymerase II transcription / 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 III transcription / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / Formation of TC-NER Pre-Incision Complex / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase I promoter / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / Estrogen-dependent gene expression / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / transcription by RNA polymerase III / Dual incision in TC-NER / translesion synthesis / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / transcription-coupled nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / ribonucleoside binding / DNA-directed RNA polymerase / cytoplasmic stress granule / DNA-directed RNA polymerase activity / peroxisome / ribosome biogenesis / nucleic acid binding / transcription by RNA polymerase II / 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 / Gyrase A; domain 2 - #140 / RPB5-like RNA polymerase subunit / N-terminal domain of TfIIb - #10 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase, RBP11-like subunit ...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 / Gyrase A; domain 2 - #140 / RPB5-like RNA polymerase subunit / N-terminal domain of TfIIb - #10 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase, RBP11-like subunit / Enzyme I; Chain A, domain 2 / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / DNA-directed RNA polymerase, insert domain / RNA Polymerase Alpha Subunit; Chain A, domain 2 / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / Gyrase A; domain 2 / 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 / Homeodomain-like / 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. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / 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. / Single Sheet / Nucleic acid-binding proteins / Beta Complex / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / 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 Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit
Similarity search - Domain/homology
Chem-2KH / 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 ...Chem-2KH / 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: 2.951 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 13, 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*CP*AP*(3DR)P*CP*TP*CP*TP*TP*GP*AP*TP*G)-3')
R: RNA (5'-R(*AP*UP*CP*AP*AP*GP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)482,37923
Polymers481,32412
Non-polymers1,05511
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area61400 Å2
ΔGint-361 kcal/mol
Surface area135580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.720, 220.430, 193.150
Angle α, β, γ (deg.)90.00, 100.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

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

#1: Protein DNA-directed RNA polymerase II subunit RPB1 / RNA polymerase II subunit 1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III ...RNA polymerase II subunit 1 / 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 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04050, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase II subunit RPB2 / RNA polymerase II subunit 2 / B150 / DNA-directed RNA polymerase II 140 kDa polypeptide


Mass: 138937.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPB2 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P08518, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase II subunit RPB3 / RNA polymerase II subunit 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 / Gene: RPB3 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P16370
#7: Protein DNA-directed RNA polymerase II subunit RPB9 / RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA- ...RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA-directed RNA polymerase II subunit 9


Mass: 14308.161 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPB9 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P27999
#9: Protein DNA-directed RNA polymerase II subunit RPB11 / RNA polymerase II subunit B11 / B13.6 / DNA-directed RNA polymerase II 13.6 kDa polypeptide


Mass: 13633.493 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPB11, YOL005C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38902

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

#4: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 ...RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 kDa polypeptide


Mass: 25117.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPB5, RPA7, RPC9, YBR154C, YBR1204 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20434
#5: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 ...RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 kDa polypeptide


Mass: 17931.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPO26, RPB6, YPR187W, P9677.8 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20435
#6: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I / and III 14.5 kDa polypeptide


Mass: 16525.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPB8, YOR224C, YOR50-14 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20436
#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I / and III 8.3 kDa polypeptide


Mass: 8290.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPB10, YOR210W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22139
#10: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha


Mass: 7729.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPC10 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40422

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DNA chain / RNA chain , 2 types, 2 molecules TR

#11: DNA chain DNA (5'-D(P*CP*AP*(3DR)P*CP*TP*CP*TP*TP*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(*AP*UP*CP*AP*AP*GP*AP*GP*A)-3')


Mass: 2918.831 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 11 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-2KH / 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3

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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: 4 Å3/Da / Density % sol: 69.22 %
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: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→95.3 Å / Num. obs: 126240 / % possible obs: 96.6 % / Redundancy: 6.5 % / Net I/σ(I): 8
Reflection shellResolution: 2.95→3.11 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.951→55.607 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.13
RfactorNum. reflection% reflection
Rfree0.2601 6424 5.09 %
Rwork0.2343 --
obs0.2356 126204 86.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.951→55.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27808 427 39 0 28274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00228826
X-RAY DIFFRACTIONf_angle_d0.56839019
X-RAY DIFFRACTIONf_dihedral_angle_d12.40211000
X-RAY DIFFRACTIONf_chiral_restr0.0224387
X-RAY DIFFRACTIONf_plane_restr0.0034971
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.951-2.98450.4808140.3842299X-RAY DIFFRACTION7
2.9845-3.01960.4974500.3708951X-RAY DIFFRACTION21
3.0196-3.05640.37741200.35781866X-RAY DIFFRACTION42
3.0564-3.09510.35611240.3522663X-RAY DIFFRACTION58
3.0951-3.13580.41730.35123314X-RAY DIFFRACTION72
3.1358-3.17880.34542030.33393955X-RAY DIFFRACTION86
3.1788-3.22420.33752240.32384475X-RAY DIFFRACTION97
3.2242-3.27230.342320.31944435X-RAY DIFFRACTION98
3.2723-3.32350.32622520.31444503X-RAY DIFFRACTION98
3.3235-3.37790.34732140.30574498X-RAY DIFFRACTION97
3.3779-3.43620.33792590.29514410X-RAY DIFFRACTION97
3.4362-3.49860.33052330.28574492X-RAY DIFFRACTION97
3.4986-3.56590.32692440.27984434X-RAY DIFFRACTION97
3.5659-3.63870.30112480.26564460X-RAY DIFFRACTION98
3.6387-3.71780.27872390.25934436X-RAY DIFFRACTION97
3.7178-3.80430.27482470.25254480X-RAY DIFFRACTION97
3.8043-3.89940.26412270.24594462X-RAY DIFFRACTION97
3.8994-4.00480.25332250.23264382X-RAY DIFFRACTION95
4.0048-4.12260.24852580.21384157X-RAY DIFFRACTION91
4.1226-4.25560.22082510.20534471X-RAY DIFFRACTION98
4.2556-4.40760.21332260.18744525X-RAY DIFFRACTION99
4.4076-4.5840.23022320.18324570X-RAY DIFFRACTION99
4.584-4.79260.19712500.17644512X-RAY DIFFRACTION98
4.7926-5.04510.21372540.18634463X-RAY DIFFRACTION98
5.0451-5.36090.20282470.20094510X-RAY DIFFRACTION98
5.3609-5.77450.21662160.21034365X-RAY DIFFRACTION94
5.7745-6.35480.25272230.22064172X-RAY DIFFRACTION91
6.3548-7.27260.26822460.21594545X-RAY DIFFRACTION98
7.2726-9.15610.19492410.17264539X-RAY DIFFRACTION98
9.1561-55.61720.22312520.19794436X-RAY DIFFRACTION95
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)
11.3548-0.1999-0.04711.19220.03460.7303-0.0663-0.13250.6038-0.244-0.04690.8667-0.6347-0.97830.04020.69810.2949-0.16881.1434-0.1171.3612413.05325.7788623.4966
20.47510.21260.17790.8677-0.08910.85490.15510.0083-0.1137-0.20930.0517-0.00020.44290.0944-0.0360.21610.1116-0.03960.1191-0.0620.17462.7518-18.7508614.0816
30.78620.00620.13241.30470.66471.02260.12740.1457-0.161-0.03670.1987-0.04450.5937-0.13570.0830.6708-0.1035-0.27360.1996-0.06590.4049443.3062-43.1127600.1611
40.0945-0.57280.46893.222-2.72262.27070.15820.10490.0728-0.9511-0.17760.08950.3226-0.04150.05351.0797-0.0746-0.26140.40030.10070.5935437.8567-3.5663564.2388
51.5439-0.31320.10321.21570.35532.67640.0907-0.14950.364-0.1820.01560.4873-0.0421-0.5923-0.06840.2993-0.1003-0.1450.3499-0.00480.5363430.0871-16.8023610.344
61.1914-0.26960.07671.11610.22221.1790.0043-0.04930.51680.09490.06720.0952-0.4943-0.1714-0.0640.44630.14680.1850.255-0.10140.3781462.008536.8998621.165
70.679-0.04691.10690.4833-0.41922.4559-0.01740.01270.2919-0.18720.06530.2256-0.2155-0.3031-0.03950.40870.160.07610.38550.03370.4749442.297829.6008591.4567
82.706-1.73750.15292.91720.07811.45880.0391-0.0293-0.0574-0.0502-0.07290.9674-0.2875-0.47810.12310.34140.11930.16080.4652-0.08990.5524444.821332.169622.5946
91.0493-0.16760.14341.2713-0.13171.37480.00460.14180.2177-0.3081-0.06530.0527-0.25130.2052-0.08690.2540.01520.17850.2258-0.02560.154468.807525.1649596.9027
100.4278-0.01060.49491.3028-0.24840.97340.1924-0.21990.10040.2862-0.10210.2298-0.1797-0.2891-0.01250.12950.0080.18840.3938-0.14880.1799463.76678.2197638.7521
110.25430.36130.33040.8384-0.01490.95220.0476-0.32680.25620.0125-0.04560.31760.142-0.1815-0.04580.09660.08250.01130.3031-0.07720.3254453.794-8.3839626.2418
126.79980.40850.52194.37961.53692.1515-0.0904-0.01460.02070.39380.0607-0.61940.17090.29510.01320.37020.2943-0.1070.8484-0.03550.4377505.5779-21.1004633.9606
131.3064-0.3172-0.06861.4963-0.0781.01330.1007-0.1637-0.03730.2887-0.0271-0.1509-0.02680.4206-0.06410.1591-0.0195-0.04310.4794-0.04350.2121488.5232-0.3303648.8422
140.2466-0.42280.15490.95620.08130.61230.16110.1328-0.0509-0.2847-0.0399-0.3150.14830.5631-0.06170.28080.2195-0.00020.5787-0.16210.4589497.557-20.0897614.2846
151.45070.35620.89542.86931.56082.03320.21050.2695-0.3484-0.312-0.0168-0.24020.20880.3073-0.22320.42280.3202-0.06560.69710.02980.5568500.9492-25.214623.2579
161.65450.02610.54722.65630.28791.40670.1152-0.5939-0.35680.70150.0816-0.35530.31720.0274-0.01350.51550.2093-0.26710.55240.12490.4616490.5054-28.1858648.3717
173.67290.5146-0.30341.44260.19313.7991-0.20810.8274-0.188-0.3130.06660.01320.1748-0.03930.05070.875-0.2423-0.4790.78320.08680.7704421.6193-28.1667568.6672
184.381.2189-1.04691.8001-0.74018.5122-0.1921.05090.3571-0.71950.08780.4267-0.6449-0.26970.15131.4783-0.4672-0.57651.49110.01960.9496419.0369-24.9221555.6783
192.09490.04111.29691.4667-0.52713.1742-0.18520.33410.2561-0.2347-0.04580.1896-0.0673-0.2551-0.04711.0006-0.3509-0.59620.94170.13011.121409.5151-32.4257575.3118
200.0898-0.11290.10330.1423-0.13560.1575-0.01480.09610.52150.1038-0.03940.2316-0.3128-0.0219-0.03281.06270.0488-0.47271.73170.54842.0649402.9424-16.9151570.9461
210.95470.8213-0.97280.9721-0.62341.6620.1670.08110.435-0.22850.1850.7890.1869-0.6999-0.09290.5432-0.2471-0.37990.50140.05560.9163417.4067-25.6796588.9278
220.4033-0.7239-0.83664.2310.07832.42560.07290.162-0.4764-0.28870.19980.86050.3727-0.6763-0.12850.8209-0.3418-0.24150.57210.15390.7378424.7655-42.9603620.0574
230.5604-0.1266-0.52563.03570.32141.10890.4427-0.5355-0.27130.7908-0.0470.14510.9834-0.058-0.23530.664-0.2246-0.1180.52180.02310.3688439.1595-37.1218638.1627
241.92830.43011.58546.15971.61012.30680.0801-0.0538-0.7985-0.13960.1918-0.26730.46630.0103-0.12680.8211-0.22760.01460.40460.10670.3874439.7973-42.0216636.1049
255.9383-1.7511.41956.6623-2.90643.1464-0.0087-0.1354-0.39390.56350.38280.3451-0.0424-0.2768-0.24570.6122-0.2738-0.14050.43290.08880.5382427.4122-39.5091623.589
261.96650.1769-1.75490.11950.00061.8085-0.04550.0996-0.1188-0.0401-0.0852-0.03980.23310.04510.15791.04840.43770.00620.6803-0.28751.1792488.6403-53.483598.7128
273.1513-0.5157-0.4684.85420.83551.9956-0.03630.399-0.2894-0.6953-0.3526-0.04420.0339-0.10540.10320.78330.4447-0.02340.6164-0.16640.8176486.3598-45.5968597.2153
280.03970.032-0.020.3913-0.35640.3272-0.11550.1756-0.2761-0.2687-0.0662-0.39280.21770.01270.11610.81090.39860.02090.7279-0.30040.8465493.1421-47.5681602.3239
290.6487-1.8143-2.47175.21997.09729.8567-0.1132-0.0698-0.48610.5188-0.11030.03870.6866-0.24510.15821.11510.3109-0.15520.5385-0.03810.8825482.8524-53.3255622.5209
303.848-0.91560.10973.3520.48713.7087-0.4784-1.01140.15541.24690.7757-0.35850.39320.4533-0.29451.41570.73030.13971.07970.14741.405492.9648-56.2428621.7012
312.3651-1.0795-0.44751.8751-0.5610.5370.16950.1922-0.4013-0.05730.0532-0.07260.19610.0855-0.07381.05660.3219-0.16130.5357-0.33790.7133480.1029-51.5262605.4059
325.1891-0.2787-0.04624.7936-0.75724.37820.04060.6299-0.8222-0.5073-0.07380.29850.7981-0.25060.13450.98290.2528-0.07660.5258-0.32850.9397475.6444-54.9448596.5421
331.7246-0.4756-1.04681.5559-0.15410.77340.15020.44-0.5332-0.6283-0.35160.42720.0573-0.18820.18920.82960.4078-0.19480.577-0.16240.4787479.591-49.0205599.6889
347.36944.18033.90817.7952-0.5313.4645-0.1077-0.8180.16750.96520.1590.1640.5636-0.0189-0.01691.30470.2634-0.17240.69-0.18890.8176476.211-59.6378604.6613
350.6516-0.3198-0.79468.1178-0.71576.15030.0665-0.04640.0534-0.36080.0148-0.5020.34930.6127-0.1150.96580.3611-0.09380.563-0.24860.9286491.2899-53.5428607.4776
360.169-0.0928-0.38452.70990.54940.9028-0.04420.0383-0.0673-0.31790.24990.3117-0.1302-0.5023-0.13881.02430.0353-0.19830.50070.19910.6186433.716530.4388559.3904
373.33330.617-0.70333.2136-0.45043.72640.21110.3657-0.0037-0.23530.04130.16440.0287-0.21-0.23750.29610.0110.05290.35220.01750.1668466.207718.6167569.8757
382.01740.5178-1.17660.7029-0.99691.53250.1329-0.1845-0.10020.1502-0.03250.0935-0.14160.22680.01210.14450.08660.01730.4743-0.08130.199489.54232.0103634.6294
397.1855-1.68730.1681.0383-0.07253.2690.0761-0.15050.88810.0942-0.2334-0.6474-0.5150.79080.11140.1999-0.15770.05780.5334-0.09490.4633497.235913.4163629.9627
403.5475-1.2501-0.21730.8697-0.30473.95940.2254-0.01140.4206-0.0794-0.1017-0.5125-0.19480.8209-0.06780.12420.07610.10410.4843-0.04690.3417495.63395.5827625.6934
417.91513.55043.25373.17220.8021.61090.0876-0.37780.6060.2821-0.10720.4753-0.1273-0.13570.06120.2007-0.09990.12340.294-0.04750.4984480.839521.4298636.2965
421.2359-1.10280.63656.2099-1.68131.06620.1766-0.1276-0.51660.0238-0.170.43010.28220.3065-0.01760.31030.0664-0.05190.4087-0.00890.2993473.3673-27.8953644.3322
432.04390.083-0.55114.276-1.58982.36650.15530.12-0.2919-0.0073-0.2361-0.64180.37390.40450.12420.51250.1874-0.15750.33870.03650.3662484.5281-34.7119637.5382
440.90380.20130.17610.3396-0.02240.43740.1558-0.2694-0.42530.0393-0.0637-0.3890.44590.3714-0.06260.44190.3048-0.23190.52630.06820.5182490.1633-32.5754639.2258
454.2257-0.62043.7453.70112.95596.82180.15-1.1011-0.54940.6902-0.23180.07740.00970.16150.10060.94280.0315-0.1640.821-0.290.867466.786324.1542654.8438
462.02831.77251.90882.27250.79932.83920.1474-0.1202-0.32470.5463-0.0651-1.67260.12262.8112-0.08620.67980.09550.07690.8392-0.13650.7985472.372930.2622647.842
475.8583-4.39014.88023.3975-3.82954.3413-0.1993-0.6816-0.3820.83450.0161.07960.5887-0.98480.11661.4146-0.08280.10511.0273-0.54991.226466.390628.0423658.189
480.4163-0.77651.32311.4992-2.4734.4128-1.4013-0.0542-1.8362-1.4739-0.152-0.89432.4120.44421.53841.85250.18560.02461.6783-0.24291.9622456.881329.103657.1491
493.4199-1.9014-3.09577.98930.11983.1722-0.2685-0.15581.0212-0.05820.06980.2089-0.68070.38740.19721.52430.0303-0.03090.768-0.48471.1707467.23936.2653651.4032
503.4839-4.3009-0.97145.85582.18532.0699-0.1687-0.33810.26080.6556-0.0395-0.0768-0.4063-0.01010.21650.4567-0.08430.01410.6367-0.10250.2086470.518614.1107651.3369
511.180.41570.80672.5784-0.0441.8396-0.25310.0569-0.16740.309-0.16350.17790.1891-0.21090.31021.52480.11750.11981.65630.12831.284446.14037.2093626.0117
520.8177-0.65490.2253.43220.47312.29040.06990.1663-0.13380.0528-0.07440.1086-0.2554-0.52480.00991.4427-0.15330.19421.50170.02841.3158448.50017.3335623.6798
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 347 )
2X-RAY DIFFRACTION2chain 'A' and (resid 348 through 845 )
3X-RAY DIFFRACTION3chain 'A' and (resid 846 through 1116 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1117 through 1340 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1341 through 1446 )
6X-RAY DIFFRACTION6chain 'B' and (resid 20 through 185 )
7X-RAY DIFFRACTION7chain 'B' and (resid 186 through 408 )
8X-RAY DIFFRACTION8chain 'B' and (resid 409 through 487 )
9X-RAY DIFFRACTION9chain 'B' and (resid 488 through 775 )
10X-RAY DIFFRACTION10chain 'B' and (resid 776 through 994 )
11X-RAY DIFFRACTION11chain 'B' and (resid 995 through 1220 )
12X-RAY DIFFRACTION12chain 'C' and (resid 3 through 26 )
13X-RAY DIFFRACTION13chain 'C' and (resid 27 through 175 )
14X-RAY DIFFRACTION14chain 'C' and (resid 176 through 209 )
15X-RAY DIFFRACTION15chain 'C' and (resid 210 through 239 )
16X-RAY DIFFRACTION16chain 'C' and (resid 240 through 268 )
17X-RAY DIFFRACTION17chain 'E' and (resid 3 through 38 )
18X-RAY DIFFRACTION18chain 'E' and (resid 39 through 54 )
19X-RAY DIFFRACTION19chain 'E' and (resid 55 through 82 )
20X-RAY DIFFRACTION20chain 'E' and (resid 83 through 103 )
21X-RAY DIFFRACTION21chain 'E' and (resid 104 through 215 )
22X-RAY DIFFRACTION22chain 'F' and (resid 72 through 86 )
23X-RAY DIFFRACTION23chain 'F' and (resid 87 through 116 )
24X-RAY DIFFRACTION24chain 'F' and (resid 117 through 132 )
25X-RAY DIFFRACTION25chain 'F' and (resid 133 through 155 )
26X-RAY DIFFRACTION26chain 'H' and (resid 3 through 16 )
27X-RAY DIFFRACTION27chain 'H' and (resid 17 through 43 )
28X-RAY DIFFRACTION28chain 'H' and (resid 44 through 60 )
29X-RAY DIFFRACTION29chain 'H' and (resid 61 through 82 )
30X-RAY DIFFRACTION30chain 'H' and (resid 83 through 92 )
31X-RAY DIFFRACTION31chain 'H' and (resid 93 through 106 )
32X-RAY DIFFRACTION32chain 'H' and (resid 107 through 118 )
33X-RAY DIFFRACTION33chain 'H' and (resid 119 through 127 )
34X-RAY DIFFRACTION34chain 'H' and (resid 128 through 140 )
35X-RAY DIFFRACTION35chain 'H' and (resid 141 through 146 )
36X-RAY DIFFRACTION36chain 'I' and (resid 2 through 52 )
37X-RAY DIFFRACTION37chain 'I' and (resid 53 through 116 )
38X-RAY DIFFRACTION38chain 'J' and (resid 1 through 17 )
39X-RAY DIFFRACTION39chain 'J' and (resid 18 through 26 )
40X-RAY DIFFRACTION40chain 'J' and (resid 27 through 55 )
41X-RAY DIFFRACTION41chain 'J' and (resid 56 through 65 )
42X-RAY DIFFRACTION42chain 'K' and (resid 1 through 29 )
43X-RAY DIFFRACTION43chain 'K' and (resid 30 through 55 )
44X-RAY DIFFRACTION44chain 'K' and (resid 56 through 114 )
45X-RAY DIFFRACTION45chain 'L' and (resid 27 through 31 )
46X-RAY DIFFRACTION46chain 'L' and (resid 32 through 36 )
47X-RAY DIFFRACTION47chain 'L' and (resid 37 through 41 )
48X-RAY DIFFRACTION48chain 'L' and (resid 42 through 46 )
49X-RAY DIFFRACTION49chain 'L' and (resid 47 through 51 )
50X-RAY DIFFRACTION50chain 'L' and (resid 52 through 70 )
51X-RAY DIFFRACTION51chain 'T' and (resid 18 through 29 )
52X-RAY DIFFRACTION52chain 'R' and (resid 1 through 9 )

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