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- PDB-3po3: Arrested RNA Polymerase II reactivation intermediate -

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Basic information

Entry
Database: PDB / ID: 3po3
TitleArrested RNA Polymerase II reactivation intermediate
Components
  • (DNA-directed RNA polymerase II subunit ...) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • DNA non-template strand
  • DNA template strand
  • RNA product strand
  • Transcription elongation factor S-II
KeywordsTRANSFERASE/DNA/RNA / RNA Polymerase II / mRNA / Transcription / arrest / backtracking / cleavage / TRANSFERASE-DNA-RNA complex
Function / homology
Function and homology information


RNA polymerase II complex recruiting activity / regulation of mRNA 3'-end processing / RPB4-RPB7 complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 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 complex recruiting activity / regulation of mRNA 3'-end processing / RPB4-RPB7 complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 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 / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / 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 / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / nucleolar large rRNA transcription by RNA polymerase I / RNA polymerase II complex binding / Estrogen-dependent gene expression / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / nuclear-transcribed mRNA catabolic process / positive regulation of translational initiation / transcription by RNA polymerase III / Dual incision in TC-NER / positive regulation of RNA polymerase II transcription preinitiation complex assembly / 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 / translation initiation factor binding / transcription-coupled nucleotide-excision repair / transcription antitermination / RNA polymerase II transcription regulatory region sequence-specific DNA binding / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / DNA-templated transcription initiation / positive regulation of transcription elongation by RNA polymerase II / ribonucleoside binding / mRNA processing / DNA-directed RNA polymerase / cytoplasmic stress granule / DNA-directed RNA polymerase activity / peroxisome / ribosome biogenesis / single-stranded DNA binding / nucleic acid binding / transcription by RNA polymerase II / single-stranded RNA binding / protein dimerization activity / nucleotide binding / mRNA binding / regulation of transcription by RNA polymerase II / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
RNA Polymerase II, Rpb4 subunit / Transcription elongation factor, TFIIS / Transcription elongation factor, IIS-type / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / TFIIS central domain profile. / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) ...RNA Polymerase II, Rpb4 subunit / Transcription elongation factor, TFIIS / Transcription elongation factor, IIS-type / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / TFIIS central domain profile. / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / RNA polymerase Rpb7-like, N-terminal domain / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / TFIIS N-terminal domain profile. / Transcription factor IIS, N-terminal / TFIIS helical bundle-like domain / DCoH-like / RNA polymerase alpha subunit dimerisation domain / Hypothetical Protein Ta0175; 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 / Gyrase A; domain 2 - #140 / RPB5-like RNA polymerase subunit / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / N-terminal domain of TfIIb - #10 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / RNA polymerase II, Rpb2 subunit, wall domain / TFIIS/LEDGF domain superfamily / 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 / Growth Hormone; Chain: A; / DNA-directed RNA polymerase, insert domain / RNA Polymerase Alpha Subunit; Chain A, domain 2 / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / Gyrase A; domain 2 / 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 / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Homeodomain-like / Zinc finger TFIIS-type signature. / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / 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
Similarity search - Domain/homology
ACETATE ION / TRIETHYLENE GLYCOL / DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB1 / Transcription elongation factor S-II / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 ...ACETATE ION / TRIETHYLENE GLYCOL / DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB1 / Transcription elongation factor S-II / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / 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 RPB7 / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / PHASER / Resolution: 3.3 Å
AuthorsCheung, A.C.M. / Cramer, P.
CitationJournal: Nature / Year: 2011
Title: Structural basis of RNA polymerase II backtracking, arrest and reactivation.
Authors: Cheung, A.C. / Cramer, P.
History
DepositionNov 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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
D: DNA-directed RNA polymerase II subunit RPB4
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
G: DNA-directed RNA polymerase II subunit RPB7
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
N: DNA non-template strand
P: RNA product strand
S: Transcription elongation factor S-II
T: DNA template strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)549,50030
Polymers548,38016
Non-polymers1,12014
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)220.019, 395.067, 280.429
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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DNA-directed RNA polymerase II subunit ... , 7 types, 7 molecules ABCDGIK

#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 natural source / Source: (natural) 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 natural source / Source: (natural) 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 natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P16370, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase II subunit RPB4 / RNA polymerase II subunit B4 / B32 / DNA-directed RNA polymerase II 32 kDa polypeptide


Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20433, DNA-directed RNA polymerase
#7: Protein DNA-directed RNA polymerase II subunit RPB7 / RNA polymerase II subunit B7 / B16


Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P34087, DNA-directed RNA polymerase
#9: 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 natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P27999, DNA-directed RNA polymerase
#11: 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 natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38902, DNA-directed RNA polymerase

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

#5: 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 / 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 natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20434, DNA-directed RNA polymerase
#6: 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 / II / and ...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 natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20435, DNA-directed RNA polymerase
#8: 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 / II / and III 14.5 kDa polypeptide


Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20436, DNA-directed RNA polymerase
#10: 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 / II / and III 8.3 kDa polypeptide


Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22139, DNA-directed RNA polymerase
#12: 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 natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40422, DNA-directed RNA polymerase

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DNA chain , 2 types, 2 molecules NT

#13: DNA chain DNA non-template strand


Mass: 4344.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesised
#16: DNA chain DNA template strand


Mass: 8323.189 Da / Num. of mol.: 1 / Mutation: E291A / Source method: obtained synthetically / Details: Chemically synthesised

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RNA chain / Protein , 2 types, 2 molecules PS

#14: RNA chain RNA product strand


Mass: 1480.952 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Enzymatically synthesised
#15: Protein Transcription elongation factor S-II / DNA strand transfer protein alpha / STP-alpha / DNA strand transferase 1 / Pyrimidine pathway ...DNA strand transfer protein alpha / STP-alpha / DNA strand transferase 1 / Pyrimidine pathway regulatory protein 2


Mass: 20072.775 Da / Num. of mol.: 1 / Mutation: D290A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DST1, PPR2, YGL043W / Production host: Escherichia coli (E. coli) / References: UniProt: P07273

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Non-polymers , 5 types, 14 molecules

#17: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#18: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#19: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#20: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#21: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4

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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: 5.56 Å3/Da / Density % sol: 77.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 4-7% PEG6000, 50mM HEPES pH 7.0, 200mM AMMONIUM ACETATE, 300mM SODIUM ACETATE, 5mM TCEP , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9188 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2010
RadiationMonochromator: Fixed-exit LN2 cooled Double Crystal Monochromator Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9188 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 181822 / Num. obs: 181822 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 9.1 / Biso Wilson estimate: 123.07 Å2
Reflection shellResolution: 3.3→3.48 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHASERphasing
BUSTER2.9.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: PHASER
Starting model: 1WCM

1wcm


Resolution: 3.3→49.97 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.9345 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.189 9121 5.02 %RANDOM
Rwork0.161 ---
obs0.1624 181822 --
all-181822 --
Displacement parametersBiso mean: 128 Å2
Baniso -1Baniso -2Baniso -3
1-9.9046 Å20 Å20 Å2
2--15.5039 Å20 Å2
3----25.4085 Å2
Refine analyzeLuzzati coordinate error obs: 0.774 Å
Refinement stepCycle: LAST / Resolution: 3.3→49.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32455 510 43 0 33008
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0133638HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.3445510HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d12209SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes896HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4738HARMONIC5
X-RAY DIFFRACTIONt_it33596HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.84
X-RAY DIFFRACTIONt_other_torsion23.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion44415
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance671
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact391254
LS refinement shellResolution: 3.3→3.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2563 679 5.08 %
Rwork0.2306 12695 -
all0.2319 13374 -
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)
15.6310.07931.77253.25250.31512.18230.14760.3499-0.36610.0416-0.04080.42470.5442-0.4549-0.1068-0.0457-0.04590.15920.29950.018-0.502496.745731.1682-37.5932
22.52520.08760.4132.91510.17612.3974-0.07160.29310.6557-0.2672-0.05790.3363-0.4374-0.31770.1295-0.23070.1672-0.01330.13480.2069-0.307590.052658.7776-41.7735
30.90520.05250.12521.0631-0.27411.35250.068-0.14350.16680.4019-0.08-0.25610.0810.25220.0120.0076-0.0270.0027-0.02820.0276-0.2921123.50236.25345.7611
40.7187-0.9023-0.74722.3813-0.26850.5182-0.1045-0.35770.45581.16770.06690.0373-0.39420.05430.03760.4023-0.02310.197-0.1886-0.269-0.1027101.83269.201126.7541
51.7010.64390.12411.09670.04610.2990.1346-0.08410.47980.3054-0.1341-0.4202-0.12720.165-0.0005-0.1853-0.0994-0.0169-0.13640.06690.1486136.94567.4383-2.1922
66.1782-4.03170.25623.3138-0.33020.36320.090.07221.1270.1226-0.1633-0.3348-0.2497-0.23710.0733-0.25890.05650.1104-0.32080.01480.600999.7916105.704-3.3535
70.7607-0.3260.52741.02480.09610.77710.06190.20540.498-0.0211-0.1373-0.0709-0.00920.02740.0755-0.2212-0.01390.1076-0.07320.1194-0.0779116.92358.9939-18.7329
81.1565-0.9626-0.27652.8559-0.24880.7060.1043-0.1257-0.01010.17530.06141.45450.0528-0.4404-0.1656-0.32970.02450.3431-0.16510.0910.43764.291245.494311.3222
97.3148-2.21671.69356.9504-1.90785.18120.25020.4163-0.1959-0.5510.0750.16990.3282-0.076-0.3252-0.3470.1690.2587-0.4419-0.10130.479764.921484.513-4.2398
102.40680.838-0.07372.50150.51670.3298-0.21730.29980.3475-0.29080.28470.8841-0.1829-0.189-0.0674-0.12460.06940.2219-0.28440.08570.072472.779652.66672.529
111.8028-1.0960.67951.9151-0.49721.2399-0.1911-0.70550.56830.84350.1320.6779-0.1526-0.54650.05910.02670.24450.6079-0.1266-0.11020.275367.478968.988427.2686
120-1.4286-0.34591.4842-0.48960.1393-0.0719-0.41950.16630.98040.20270.4986-0.0066-0.2112-0.13090.2894-0.02660.3473-0.0336-0.0849-0.227190.678742.467924.0281
133.19630.57732.04293.56531.13056.2998-0.0250.3595-0.3124-0.56870.20960.94870.243-0.2229-0.18460.0721-0.12980.0527-0.23130.0675-0.138283.551717.466-0.0463
140.9588-0.0194-0.11930.9025-0.16671.65520.04-0.05520.12960.3730.02310.10410.0713-0.0322-0.06310.00050.02780.1175-0.13620.0101-0.307106.345382.4769
151.19920.03470.02591.64580.05190.7286-0.0994-0.4042-0.22860.86070.12630.16220.14940.0502-0.02690.61670.04990.1980.0430.1347-0.5697107.8415.845136.3952
162.06010.43050.60451.4708-0.90664.2997-0.1330.0049-0.05710.13630.0618-0.20150.19830.74570.0711-0.11650.24120.05040.3263-0.086-0.3431135.18429.0727-64.3436
171.4063-0.3629-0.37593.73640.36832.14570.19490.55450.868-0.8601-0.138-0.0877-0.7259-0.058-0.0569-0.2178-0.04480.176-0.28250.42670.3249125.53491.9989-27.2101
183.6674-1.2670.83186.1928-1.08523.46610.08870.10790.2384-0.0871-0.172-0.40830.4150.31110.0833-0.09480.05840.03860.13510.072-0.2216137.7938.2817-18.7588
190.55460.64741.08781.0272.05485.9867-0.04240.1543-0.33630.18050.16430.00990.75360.4246-0.12190.04380.26230.09160.1960.0099-0.2748125.44422.6145-58.7718
206.0231.36570.83335.060.15332.632-0.0686-0.69220.29570.8116-0.0031-1.1824-0.22680.77870.07170.121-0.2148-0.51920.0634-0.1188-0.3531150.57350.900837.1371
210.6351-0.0278-0.20981.7946-0.69350.0358-0.21610.18020.54380.63510.0930.4678-0.154-0.17280.12310.01870.27170.457-0.4065-0.23820.372675.384199.976914.539
222.3038-1.4875-0.58252.6404-0.94042.3786-0.0663-0.5663-0.10341.04750.17580.32710.079-0.1246-0.10950.55770.00370.49650.03830.0745-0.388488.537525.699837.8441
232.53180.64170.26072.24190.01871.5981-0.1265-0.3393-0.21180.8473-0.0291-0.5970.33240.38570.15560.47090.1113-0.12910.150.0748-0.3208129.31716.566328.2559
2410.14611.61885.61191.88591.49265.22870.1961-0.1248-0.28290.2129-0.15171.28490.665-0.4056-0.0444-0.0041-0.28080.2416-0.30860.24540.251573.248410.35349.4926
253.3881-0.34822.51816.28630.52784.2263-0.04360.27610.540.31550.03470.2578-0.60770.29830.0089-0.1084-0.2314-0.2156-0.35950.13340.9422104.329132.6782.0841
260.42191.0122-0.82530.33020.82252.6058-0.0722-0.21250.48830.2709-0.04750.0847-0.11830.20460.1197-0.0921-0.01340.0046-0.4133-0.20540.4774106.305100.02614.0693
270.5173-6.0286-2.10320.01820.04546.2510.1506-0.03650.3121-0.45-0.1002-0.3467-0.14680.2719-0.05040.32610.15340.0233-0.1683-0.0676-0.0724115.37766.339516.2528
282.0364-2.8061-1.6982.82433.39650-0.01770.04450.0263-0.05750.00410.0302-0.0633-0.05950.01360.15680.0697-0.04640.0302-0.0285-0.102693.592670.0965-18.1739
291.0722-7.91934.18480.5514-3.75540-0.0015-0.03330.2645-0.0789-0.19680.4538-0.2725-0.2290.1983-0.00980.04210.0707-0.05920.01110.201690.89668.3611-19.4004
300-1.67091.49120.4459-0.75493.33850.0328-0.1831-0.05660.05240.0960.06130.1477-0.0273-0.12880.3355-0.09180.0142-0.1718-0.02110.103198.872343.7678-3.2989
310-0.998-0.28341.5955-4.59972.6990.0152-0.0244-0.01950.012-0.02470.0384-0.10710.04170.00950.0579-0.14220.08430.1649-0.0416-0.144195.723344.96273.8903
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|3 - A|81 }A3 - 81
2X-RAY DIFFRACTION2{ A|82 - A|323 }A82 - 323
3X-RAY DIFFRACTION3{ A|324 - A|659 }A324 - 659
4X-RAY DIFFRACTION4{ A|660 - A|831 }A660 - 831
5X-RAY DIFFRACTION5{ A|832 - A|1127 }A832 - 1127
6X-RAY DIFFRACTION6{ A|1128 - A|1329 }A1128 - 1329
7X-RAY DIFFRACTION7{ A|1330 - A|1454 }A1330 - 1454
8X-RAY DIFFRACTION8{ B|20 - B|234 }B20 - 234
9X-RAY DIFFRACTION9{ B|235 - B|392 }B235 - 392
10X-RAY DIFFRACTION10{ B|393 - B|539 }B393 - 539
11X-RAY DIFFRACTION11{ B|540 - B|735 }B540 - 735
12X-RAY DIFFRACTION12{ B|736 - B|841 }B736 - 841
13X-RAY DIFFRACTION13{ B|842 - B|974 }B842 - 974
14X-RAY DIFFRACTION14{ B|975 - B|1224 }B975 - 1224
15X-RAY DIFFRACTION15{ C|3 - C|268 }C3 - 268
16X-RAY DIFFRACTION16{ D|4 - D|221 }D4 - 221
17X-RAY DIFFRACTION17{ E|2 - E|215 }E2 - 215
18X-RAY DIFFRACTION18{ F|72 - F|155 }F72 - 155
19X-RAY DIFFRACTION19{ G|1 - G|171 }G1 - 171
20X-RAY DIFFRACTION20{ H|2 - H|146 }H2 - 146
21X-RAY DIFFRACTION21{ I|2 - I|120 }I2 - 120
22X-RAY DIFFRACTION22{ J|1 - J|65 }J1 - 65
23X-RAY DIFFRACTION23{ K|2 - K|114 }K2 - 114
24X-RAY DIFFRACTION24{ L|25 - L|70 }L25 - 70
25X-RAY DIFFRACTION25{ S|146 - S|239 }S146 - 239
26X-RAY DIFFRACTION26{ S|240 - S|264 }S240 - 264
27X-RAY DIFFRACTION27{ S|265 - S|309 }S265 - 309
28X-RAY DIFFRACTION28{ N|2 - N|8 }N2 - 8
29X-RAY DIFFRACTION29{ T|10 - T|17 }T10 - 17
30X-RAY DIFFRACTION30{ T|18 - T|22 }T18 - 22
31X-RAY DIFFRACTION31{ P|7 - P|11 }P7 - 11

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