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- PDB-6bm2: Pol II elongation complex with an abasic lesion at i-1 position -

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Basic information

Entry
Database: PDB / ID: 6bm2
TitlePol II elongation complex with an abasic lesion at i-1 position
Components
  • (DNA-directed RNA polymerase II subunit ...Polymerase) x 5
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 5
  • DNA (5'-D(P*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 / termination of RNA polymerase II transcription / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes ...RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / : / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / termination of RNA polymerase II transcription / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / Estrogen-dependent gene expression / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Dual incision in TC-NER / RNA polymerase I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / tRNA transcription by RNA polymerase III / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription elongation by RNA polymerase I / RNA polymerase II activity / transcription-coupled nucleotide-excision repair / translesion synthesis / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / RNA polymerase II, core complex / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / peroxisome / ribosome biogenesis / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / N-terminal domain of TfIIb - #10 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 ...Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / N-terminal domain of TfIIb - #10 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Gyrase A; domain 2 / Zinc finger TFIIS-type signature. / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit Rpo11 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerases L / 13 to 16 Kd subunits signature. / Homeodomain-like / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Single Sheet / Nucleic acid-binding proteins / Beta Complex / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / DNA-directed RNA polymerase, insert domain
Similarity search - Domain/homology
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 / DNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.403 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)481,87221
Polymers481,32412
Non-polymers5489
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60990 Å2
ΔGint-397 kcal/mol
Surface area136290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.110, 222.270, 193.710
Angle α, β, γ (deg.)90.00, 101.28, 90.00
Int Tables number5
Space group name H-MC121

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Components

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

#1: Protein DNA-directed RNA polymerase II subunit RPB1 / Polymerase / RNA polymerase II subunit 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 / Polymerase / RNA polymerase II subunit 2 / B150 / DNA-directed RNA polymerase II 140 kDa polypeptide


Mass: 138937.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPB2 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P08518, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase II subunit RPB3 / Polymerase / RNA polymerase II subunit 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, YIL021W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P16370
#7: Protein DNA-directed RNA polymerase II subunit RPB9 / Polymerase / RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA- ...RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA-directed RNA polymerase II subunit 9


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


Mass: 13633.493 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPB11, 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 polymerase / RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / II / and ...RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / II / 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 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20434
#5: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerase / Short name: RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I ...Short name: RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / II / 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 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20435
#6: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase / RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I / and III 14.5 kDa polypeptide


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


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


Mass: 7729.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPC10, RPB12, YHR143W-A, YHR143BW / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40422

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

#11: DNA chain DNA (5'-D(P*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 , 2 types, 9 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.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 3.71 Å3/Da / Density % sol: 66.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 50mM dioxane, 10mM DTT, 9-12% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→95.9 Å / Num. obs: 83778 / % possible obs: 99.7 % / Redundancy: 3.6 % / Net I/σ(I): 5.2
Reflection shellResolution: 3.4→3.58 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 3.403→82.922 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.88
RfactorNum. reflection% reflection
Rfree0.2438 4078 4.87 %
Rwork0.219 --
obs0.2203 83759 87.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.403→82.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27808 427 9 0 28244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00228796
X-RAY DIFFRACTIONf_angle_d0.52238972
X-RAY DIFFRACTIONf_dihedral_angle_d10.96410984
X-RAY DIFFRACTIONf_chiral_restr0.0214383
X-RAY DIFFRACTIONf_plane_restr0.0024970
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4034-3.44350.297170.2754210X-RAY DIFFRACTION7
3.4435-3.48550.3029380.2885601X-RAY DIFFRACTION20
3.4855-3.52960.3292710.29371202X-RAY DIFFRACTION38
3.5296-3.5760.2843810.3031687X-RAY DIFFRACTION53
3.576-3.6250.32931090.29071986X-RAY DIFFRACTION64
3.625-3.67680.31361310.27732345X-RAY DIFFRACTION74
3.6768-3.73170.32311300.27532634X-RAY DIFFRACTION84
3.7317-3.790.29641430.28272931X-RAY DIFFRACTION93
3.79-3.85210.26841690.26853126X-RAY DIFFRACTION100
3.8521-3.91860.31631410.25943137X-RAY DIFFRACTION100
3.9186-3.98980.27441620.25243175X-RAY DIFFRACTION100
3.9898-4.06660.23721660.23843111X-RAY DIFFRACTION100
4.0666-4.14960.26171360.23033155X-RAY DIFFRACTION100
4.1496-4.23980.2581490.22213167X-RAY DIFFRACTION100
4.2398-4.33840.23821830.20733132X-RAY DIFFRACTION100
4.3384-4.44690.25221560.19853126X-RAY DIFFRACTION100
4.4469-4.56710.22021390.19523135X-RAY DIFFRACTION100
4.5671-4.70150.20731580.18683170X-RAY DIFFRACTION100
4.7015-4.85320.20131630.1873162X-RAY DIFFRACTION100
4.8532-5.02670.2241390.1973148X-RAY DIFFRACTION100
5.0267-5.22790.24351660.20513152X-RAY DIFFRACTION100
5.2279-5.46580.24741850.20913107X-RAY DIFFRACTION100
5.4658-5.75390.26441770.21663144X-RAY DIFFRACTION100
5.7539-6.11430.24521790.21813138X-RAY DIFFRACTION100
6.1143-6.58620.24571570.2253136X-RAY DIFFRACTION100
6.5862-7.24860.25951460.20933157X-RAY DIFFRACTION99
7.2486-8.29670.19111550.1813167X-RAY DIFFRACTION100
8.2967-10.44970.16611780.1523123X-RAY DIFFRACTION99
10.4497-82.94620.19931640.20453217X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4564-0.45770.52393.1117-0.17912.1681-0.2832-0.36760.71670.4158-0.17140.8417-0.5976-0.98830.36740.63290.21050.03751.3122-0.25071.1651412.9575.7474636.9735
20.7689-0.08380.08010.8036-0.12090.9372-0.22170.13610.7323-0.47330.02190.6385-0.6454-0.95150.02790.91660.3853-0.25991.4249-0.02171.714404.296410.3532616.1109
31.4937-0.0223-0.06751.09930.32681.61440.1871-0.14660.0716-0.0048-0.05340.11380.2586-0.18580.00540.28390.01-0.0810.09130.01250.1614451.8271-18.2683631.1358
40.10970.22020.02280.8318-0.39810.78220.10210.1786-0.1232-0.3250.0427-0.0090.26980.1488-0.10030.36510.0920.00140.2463-0.06920.1557465.2034-9.285598.3548
50.7923-0.01450.0551.75640.66240.91810.09080.1276-0.1922-0.08840.1269-0.01750.5531-0.06-0.00180.657-0.0428-0.23890.1818-0.06010.3635441.07-40.4172601.1852
60.33-1.29360.98245.8207-4.17623.12940.28560.2103-0.0846-1.1105-0.28520.29680.58450.08510.03761.1113-0.0279-0.26460.38640.05450.6139434.21666.5097559.1213
70.88360.1933-0.47841.2370.3912.7074-0.14090.19880.1066-0.69120.1014-0.0898-0.1850.0575-0.00580.6095-0.1632-0.19680.27220.09040.3942438.7269-18.5623587.0072
81.7827-0.3498-0.030.7051.33043.2727-0.0074-0.28170.3005-0.2378-0.0220.536-0.2276-0.95850.0650.315-0.0633-0.07120.5492-0.03720.6656422.4198-11.5504617.7386
90.6041-0.10970.39340.86790.04571.3448-0.023-0.17670.3249-0.12870.00110.2267-0.4105-0.2998-0.02410.43910.10470.21320.1755-0.07650.2894457.761335.6877619.1458
100.46820.13350.69480.2403-0.19221.6280.0226-0.13950.2753-0.06410.07080.3061-0.182-0.607-0.11010.37550.16490.09520.4198-0.00390.4946440.476331.971598.8555
111.09410.07150.07751.4389-0.05781.2970.04770.28320.2432-0.362-0.05910.0879-0.38730.282-0.13960.35860.01820.29660.2405-0.01130.1092468.133130.1979596.0569
121.1005-0.14160.05161.38440.06811.27090.14-0.20930.09550.3873-0.12180.2194-0.1266-0.2727-0.11280.20260.04310.11540.3332-0.11510.1238461.361211.0694639.9142
130.28670.30160.44730.91450.08950.82950.0063-0.34010.2787-0.0181-0.0470.36330.1161-0.2489-0.06770.07780.0773-0.00110.3463-0.11090.3189451.4231-5.622627.2997
148.01730.53091.35955.10423.20812.8059-0.0370.0254-0.00660.3782-0.0031-0.45950.10770.31610.05580.33860.2482-0.15080.87070.03810.4225503.3132-18.3127635.2662
150.62590.04-0.00940.0222-0.01910.01790.0128-0.0511-0.37450.01230.09210.00190.11020.1218-0.38040.20690.2171-0.15710.4422-0.12360.3057486.3284-11.297643.2804
161.4807-0.2337-0.19882.6616-0.22891.3602-0.1124-0.35230.12990.45670.0031-0.3701-0.08280.35240.0720.2119-0.0796-0.09130.5121-0.08260.1667486.30256.5878652.3381
170.55950.13310.38951.6791.03691.5730.24910.2168-0.21150.0358-0.0392-0.43220.36230.5329-0.18670.31220.1852-0.04510.506-0.10750.3593492.6866-15.0268622.0053
181.8508-0.33680.67421.74970.28421.69410.1294-0.0167-0.3770.2790.167-0.30830.42980.358-0.22690.4120.2059-0.27680.55910.0390.4917493.547-23.9008636.7488
192.3198-0.2265-0.09541.20070.05755.0212-0.12521.2047-0.0954-0.77940.28060.13030.02870.0177-0.09541.1193-0.2919-0.50740.92890.1080.7096418.7857-24.5272565.6653
202.61170.60811.30452.0588-0.66843.5775-0.27620.20620.3729-0.4124-0.0950.23760.2235-0.4420.20260.9447-0.3318-0.4990.7750.01381.0974408.5324-31.1165574.6566
215.74210.01361.5150.70340.95341.6818-0.12330.80871.0449-0.1639-0.0350.3034-0.505-0.32350.07120.9364-0.116-0.64151.01960.22431.3938406.525-21.5001574.637
220.7004-0.74210.22950.9913-0.7911.8605-0.3107-0.13280.6361-0.3381-0.2340.4336-0.4297-0.23960.3441.04430.0638-0.6752.06060.47882.1837397.8614-16.2536573.3281
231.57770.6706-0.53381.3274-0.74482.57740.1771-0.02150.4351-0.37760.18321.0106-0.0111-0.8851-0.22260.5763-0.1744-0.32030.43140.07390.8517415.1812-23.034589.7642
243.0485-0.0449-1.81384.99650.52093.80440.33940.4315-0.987-0.7533-0.30131.13350.9382-1.52330.00580.8712-0.2001-0.29730.7880.01230.6568422.4559-40.2931621.006
253.76080.0493-0.22584.1199-0.08884.27390.5086-1.0138-0.21450.3186-0.37920.08830.4106-0.2409-0.27990.4289-0.24720.00080.39690.05520.4082434.2611-31.2193635
268.8387-2.6092-1.52922.7622-1.86612.9619-0.1847-0.2377-0.27820.3712-0.07110.26640.10860.39810.16330.9647-0.2827-0.20520.7033-0.00510.583440.1898-39.1625645.2664
277.19470.57074.52338.3982.31084.69770.26380.1281-1.4083-0.26520.2479-0.54680.83630.0955-0.36210.7255-0.25230.08720.3935-0.03220.364437.3673-39.4009637.1757
289.4205-5.553.23353.9238-2.44276.4715-0.2525-0.5478-0.04511.03160.58070.2896-0.3017-1.1094-0.39090.8214-0.0688-0.06730.49140.08510.2764422.5893-33.4486626.4122
293.6865-2.07071.78226.2605-3.17972.73580.1396-0.3083-0.67080.44960.17460.47920.0588-0.4761-0.07590.3464-0.2320.11840.52260.10820.6422419.6319-34.6653622.1367
309.37082.51761.40913.03421.36881.73060.4522-0.29550.29510.8842-0.0298-0.55510.37810.0898-0.45050.7705-0.2985-0.11490.45570.13240.7126433.5742-42.0831626.4037
311.3211-0.236-1.00650.15240.50761.7409-0.05840.0710.1616-0.059-0.081-0.00760.0574-0.01330.1191.00560.3603-0.01660.5623-0.32561.1562486.5002-50.8638599.8737
325.1915-0.4883-0.63065.03050.31143.67740.16130.5509-0.3947-0.7783-0.37710.10710.3233-0.15470.20530.81030.4586-0.08020.6509-0.16840.7559484.2155-42.8935598.3464
330.91020.1263-0.21281.3843-0.97210.6991-0.19790.2161-0.3327-0.3995-0.0907-0.59720.46260.1102-0.05240.79840.34740.05280.6367-0.35790.8992491.0618-44.8911603.5192
341.1674-2.6122-2.69247.52486.53717.7302-0.3785-0.1491-0.50750.9528-0.00760.0891.08990.01610.36051.19420.1838-0.20960.442-0.05480.9456480.6485-50.6855623.654
357.2638-1.05421.34768.2404-1.97321.3631-0.3406-1.04220.01811.2590.7622-0.18580.50150.0855-0.35551.48110.72450.0231.07340.24011.6616490.7163-53.5167623.0213
363.0503-0.7335-0.52524.05040.4941.970.19130.2528-0.4410.0432-0.05490.11330.33110.027-0.19840.81910.1651-0.08510.4571-0.38190.7341477.9228-48.8941606.5575
374.29331.53930.01386.93550.69067.2617-0.40790.61-0.8504-0.83010.00790.18070.9446-0.41630.43761.02770.1983-0.15810.6031-0.43120.9943473.4765-52.3121597.6601
380.35880.08090.16910.01830.03840.07940.42530.9905-0.6416-0.6682-0.38040.44560.41410.4262-0.25420.77330.4242-0.290.7865-0.24080.5676477.4315-46.3911600.7813
397.82461.1649-0.89938.19064.19512.52380.186-0.84910.0011.060.45890.09870.02550.217-0.54361.32640.275-0.31470.6804-0.17780.9448474.0429-56.9561605.8331
400.5331-0.8103-0.25782.4686-1.92834.48210.0862-0.00890.0437-0.5238-0.2935-0.55110.6810.55540.05330.97520.29480.03850.4065-0.13470.9757489.085-50.9755608.6952
410.7874-0.0002-0.7234.88751.34831.0339-0.28820.067-0.1704-0.38770.3910.5409-0.3105-0.3069-0.1130.95340.0068-0.1790.42440.17960.5498431.584733.4128560.3234
424.85971.439-0.78935.4613-0.29035.70850.51340.1763-0.00570.079-0.20450.13540.0445-0.2511-0.30730.22430.03430.02170.4710.0580.1672464.089921.5665570.8738
434.18412.56010.51241.81251.64057.21780.5313-0.1419-0.48910.05530.16010.0627-0.13420.197-0.54890.16410.030.02870.3135-0.11280.4451485.99674.1466635.589
448.0442-1.53040.51341.6321.95138.6290.1199-0.09140.8705-0.187-0.0274-0.4268-0.78970.9525-0.15150.1889-0.0610.15980.42450.02110.4815494.584514.6389632.439
455.0602-0.3826-1.56957.835-6.88759.04130.0488-0.62060.88430.5391-0.2773-0.0159-0.5660.3610.21610.3706-0.23630.03180.94830.15820.772501.093617.7212625.1324
464.6962.7325-4.91136.2607-1.44445.56380.0154-0.0292-0.016-0.1994-0.0506-0.28470.04790.2150.0090.4773-0.03170.16060.60540.11820.2599498.10949.5215625.1574
471.99130.5053-0.75040.1551-0.08010.73880.0476-0.0112-0.0794-0.0617-0.015-0.12480.00580.19730.11120.1020.11260.08790.3939-0.0040.1946488.88715.9757628.2691
487.13395.13852.96034.74561.96162.13610.2817-0.4210.8620.4637-0.25890.8292-0.1564-0.19670.30110.2506-0.0894-0.00690.2109-0.01670.5549478.431124.9624637.9362
490.22160.0925-0.36412.61090.66420.85790.0928-0.3448-0.03020.284-0.18230.2890.1240.1392-0.22290.24870.12420.08860.35860.02470.1597469.0265-10.8379644.9274
503.3404-1.74861.29913.39651.34612.15910.2327-0.3825-0.36591.21990.0650.68880.6563-0.0584-0.24260.7590.11160.07670.3254-0.04110.334472.5486-21.9929651.4846
516.0578-1.48852.1265.5282-0.59183.33180.0481-0.1045-0.5328-0.14350.11250.65420.36520.1004-0.2430.63750.1344-0.17380.49320.23330.5298471.9935-36.102646.1877
520.3910.273-1.03838.3883-1.38412.80990.0358-0.3075-0.55150.04570.04570.76830.2482-0.0594-0.07780.77360.3164-0.29070.6532-0.03670.6689470.9592-44.907636.971
530.9725-1.6765-0.50126.86430.81321.19260.1029-0.0335-0.1785-0.050.14230.06270.122-0.09210.15980.51430.1247-0.20420.35870.11150.3573475.5629-29.4495642.949
541.86040.1250.23410.75740.68342.3108-0.1542-0.1974-0.0874-0.0829-0.2503-0.09640.0260.5991-0.00410.3590.1364-0.21320.31260.06670.4777484.7937-29.3051636.7325
552.0001-1.23633.57674.7964-3.16276.6212-0.1001-0.3185-1.093-0.083-0.1501-1.1061.21260.89730.27340.81120.302-0.10640.4550.0321.0527489.4004-42.0702635.0418
560.37340.2865-0.11870.3895-0.33660.39320.17560.0919-0.18930.0485-0.1802-0.19180.31550.4082-0.14860.63860.1917-0.34290.4314-0.07130.4743479.08-36.2033633.6572
571.4321-1.10611.14651.2498-1.20211.1715-0.0388-0.1627-0.15480.0823-0.0263-0.04840.21870.2175-0.17320.43040.0616-0.16790.16760.02830.224469.5167-20.8379636.8412
582.26140.0941-0.37990.97440.41330.71830.0473-0.3745-0.52330.2425-0.0167-0.26180.35350.4090.00590.76640.2218-0.22310.43880.13240.3516478.2548-39.7308639.4078
591.39260.14250.53430.09570.35321.41840.1962-0.3533-0.68120.1350.1284-0.43840.53020.5319-0.05060.39630.2612-0.04640.68680.06350.7949495.9617-28.9032643.8569
604.4762-3.82280.76593.3455-0.82250.4814-0.0235-0.3986-0.21340.21570.0733-0.63260.06820.30480.03750.30240.1486-0.08641.0096-0.06810.7935511.6592-11.3467640.6239
617.6386-1.18995.51133.873-3.4255.85410.7312-1.35370.73551.1488-0.64350.3646-1.84791.0023-0.09861.0228-0.04280.08620.9925-0.39170.7847465.784930.1492654.9872
620.3596-1.22390.90356.8141-5.4884.5986-2.1698-0.1304-2.6948-2.3544-0.5775-1.76663.19391.7172.74071.6120.3230.4551.6735-0.03521.7612454.347431.9614658.2113
633.2695-3.58250.07694.68350.78744.1422-0.2682-0.52740.63380.63380.1622-0.7016-0.7097-0.39250.37130.2860.0406-0.2020.5682-0.1720.2895467.297921.7302652.5693
642.0896-0.01881.43352.7855-1.28812.5972-0.7793-0.1727-0.02060.3328-0.16910.13710.34960.18610.89221.37840.19650.1811.42070.37981.1038444.08910.2403627.14
654.7824-1.03210.87016.8851.29054.563-0.1776-0.5962-0.19830.34330.03820.6803-0.111-0.40310.10021.1035-0.20370.09021.20060.24920.9181446.120910.1861624.6085
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 105 )
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 304 )
3X-RAY DIFFRACTION3chain 'A' and (resid 305 through 590 )
4X-RAY DIFFRACTION4chain 'A' and (resid 591 through 844 )
5X-RAY DIFFRACTION5chain 'A' and (resid 845 through 1116 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1117 through 1280 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1281 through 1376 )
8X-RAY DIFFRACTION8chain 'A' and (resid 1377 through 1446 )
9X-RAY DIFFRACTION9chain 'B' and (resid 20 through 241 )
10X-RAY DIFFRACTION10chain 'B' and (resid 242 through 533 )
11X-RAY DIFFRACTION11chain 'B' and (resid 534 through 775 )
12X-RAY DIFFRACTION12chain 'B' and (resid 776 through 994 )
13X-RAY DIFFRACTION13chain 'B' and (resid 995 through 1220 )
14X-RAY DIFFRACTION14chain 'C' and (resid 3 through 26 )
15X-RAY DIFFRACTION15chain 'C' and (resid 27 through 51 )
16X-RAY DIFFRACTION16chain 'C' and (resid 52 through 162 )
17X-RAY DIFFRACTION17chain 'C' and (resid 163 through 209 )
18X-RAY DIFFRACTION18chain 'C' and (resid 210 through 268 )
19X-RAY DIFFRACTION19chain 'E' and (resid 3 through 54 )
20X-RAY DIFFRACTION20chain 'E' and (resid 55 through 71 )
21X-RAY DIFFRACTION21chain 'E' and (resid 72 through 89 )
22X-RAY DIFFRACTION22chain 'E' and (resid 90 through 103 )
23X-RAY DIFFRACTION23chain 'E' and (resid 104 through 215 )
24X-RAY DIFFRACTION24chain 'F' and (resid 72 through 86 )
25X-RAY DIFFRACTION25chain 'F' and (resid 87 through 103 )
26X-RAY DIFFRACTION26chain 'F' and (resid 104 through 116 )
27X-RAY DIFFRACTION27chain 'F' and (resid 117 through 132 )
28X-RAY DIFFRACTION28chain 'F' and (resid 133 through 137 )
29X-RAY DIFFRACTION29chain 'F' and (resid 138 through 147 )
30X-RAY DIFFRACTION30chain 'F' and (resid 148 through 155 )
31X-RAY DIFFRACTION31chain 'H' and (resid 3 through 16 )
32X-RAY DIFFRACTION32chain 'H' and (resid 17 through 43 )
33X-RAY DIFFRACTION33chain 'H' and (resid 44 through 60 )
34X-RAY DIFFRACTION34chain 'H' and (resid 61 through 82 )
35X-RAY DIFFRACTION35chain 'H' and (resid 83 through 92 )
36X-RAY DIFFRACTION36chain 'H' and (resid 93 through 106 )
37X-RAY DIFFRACTION37chain 'H' and (resid 107 through 118 )
38X-RAY DIFFRACTION38chain 'H' and (resid 119 through 127 )
39X-RAY DIFFRACTION39chain 'H' and (resid 128 through 140 )
40X-RAY DIFFRACTION40chain 'H' and (resid 141 through 146 )
41X-RAY DIFFRACTION41chain 'I' and (resid 2 through 52 )
42X-RAY DIFFRACTION42chain 'I' and (resid 53 through 116 )
43X-RAY DIFFRACTION43chain 'J' and (resid 1 through 14 )
44X-RAY DIFFRACTION44chain 'J' and (resid 15 through 26 )
45X-RAY DIFFRACTION45chain 'J' and (resid 27 through 31 )
46X-RAY DIFFRACTION46chain 'J' and (resid 32 through 38 )
47X-RAY DIFFRACTION47chain 'J' and (resid 39 through 56 )
48X-RAY DIFFRACTION48chain 'J' and (resid 57 through 65 )
49X-RAY DIFFRACTION49chain 'K' and (resid 1 through 9 )
50X-RAY DIFFRACTION50chain 'K' and (resid 10 through 18 )
51X-RAY DIFFRACTION51chain 'K' and (resid 19 through 23 )
52X-RAY DIFFRACTION52chain 'K' and (resid 24 through 29 )
53X-RAY DIFFRACTION53chain 'K' and (resid 30 through 39 )
54X-RAY DIFFRACTION54chain 'K' and (resid 40 through 50 )
55X-RAY DIFFRACTION55chain 'K' and (resid 51 through 55 )
56X-RAY DIFFRACTION56chain 'K' and (resid 56 through 62 )
57X-RAY DIFFRACTION57chain 'K' and (resid 63 through 69 )
58X-RAY DIFFRACTION58chain 'K' and (resid 70 through 82 )
59X-RAY DIFFRACTION59chain 'K' and (resid 83 through 109 )
60X-RAY DIFFRACTION60chain 'K' and (resid 110 through 114 )
61X-RAY DIFFRACTION61chain 'L' and (resid 27 through 41 )
62X-RAY DIFFRACTION62chain 'L' and (resid 42 through 46 )
63X-RAY DIFFRACTION63chain 'L' and (resid 47 through 70 )
64X-RAY DIFFRACTION64chain 'T' and (resid 18 through 29 )
65X-RAY DIFFRACTION65chain 'R' and (resid 1 through 9 )

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