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- PDB-3po2: Arrested RNA Polymerase II elongation complex -

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Basic information

Entry
Database: PDB / ID: 3po2
TitleArrested RNA Polymerase II elongation complex
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
KeywordsTRANSFERASE/DNA/RNA / RNA Polymerase II / mRNA / Transcription / arrest / backtracking / cleavage / TRANSFERASE-DNA-RNA complex
Function / homology
Function and homology information


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 / TP53 Regulates Transcription of DNA Repair Genes ...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 / 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 II transcription / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / : / Formation of TC-NER Pre-Incision Complex / : / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / transcription by RNA polymerase III / Dual incision in TC-NER / transcription elongation by RNA polymerase I / positive regulation of translational initiation / RNA polymerase I complex / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase I activity / translesion synthesis / RNA polymerase II activity / translation initiation factor binding / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / cytoplasmic stress granule / DNA-directed RNA polymerase / peroxisome / ribosome biogenesis / single-stranded DNA binding / transcription by RNA polymerase II / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / nucleotide binding / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb7-like, N-terminal domain / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / 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 / RPB5-like RNA polymerase subunit ...RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb7-like, N-terminal domain / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / 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 / RPB5-like RNA polymerase subunit / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase II, Rpb2 subunit, wall domain / 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 / Growth Hormone; Chain: A; / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / 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 / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Gyrase A; domain 2 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / RNA polymerase subunit Rpb7-like / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / 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, 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 / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / Homeodomain-like / 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 / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / 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. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Single Sheet
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / RNA / RNA (> 10) / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 ...ACETATE ION / DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / RNA / RNA (> 10) / DNA-directed RNA polymerase II subunit RPB1 / 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 / MOLECULAR REPLACEMENT / 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_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_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
T: DNA template strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)532,29427
Polymers531,34315
Non-polymers95112
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)224.570, 394.550, 282.140
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: 4328.841 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesised
#15: DNA chain DNA template strand


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

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RNA chain , 1 types, 1 molecules P

#14: RNA chain RNA product strand


Mass: 4532.769 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Enzymatically synthesised

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Non-polymers , 5 types, 12 molecules

#16: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#17: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#19: 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
#20: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3

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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: 5.88 Å3/Da / Density % sol: 79.09 %
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: Mar 30, 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: 186691 / Num. obs: 186691 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 9.3 / Biso Wilson estimate: 119.6 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: MOLECULAR REPLACEMENT
Starting model: 1WCM

1wcm


Resolution: 3.3→48.98 Å / Cor.coef. Fo:Fc: 0.9451 / Cor.coef. Fo:Fc free: 0.9323 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1778 3689 1.98 %RANDOM
Rwork0.1532 ---
obs0.1537 186691 --
all-186691 --
Displacement parametersBiso mean: 123.79 Å2
Baniso -1Baniso -2Baniso -3
1-13.6833 Å20 Å20 Å2
2--16.8644 Å20 Å2
3----30.5477 Å2
Refine analyzeLuzzati coordinate error obs: 0.723 Å
Refinement stepCycle: LAST / Resolution: 3.3→48.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31275 977 35 0 32287
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0132949HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.3444677HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d12065SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes860HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4593HARMONIC5
X-RAY DIFFRACTIONt_it32913HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion23.54
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion43535
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance581
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact376374
LS refinement shellResolution: 3.3→3.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2416 258 1.88 %
Rwork0.2327 13433 -
all0.2328 13691 -
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)
14.9536-0.10231.35422.2117-0.2912.31250.05170.5277-0.2777-0.10650.02540.30330.4718-0.3077-0.07710.12460.00690.1090.31030.0193-0.393799.6931.8836-37.7167
22.90070.85460.24463.683-0.28882.5384-0.16590.52730.7808-0.36-0.0540.5942-0.3664-0.31690.2199-0.24040.1577-0.10170.0560.278-0.255992.312559.6059-40.8498
30.91870.0970.17220.9422-0.25941.21780.0224-0.10130.17660.2582-0.0628-0.21510.04690.17010.04040.0405-0.00740.0079-0.05140.0519-0.1973126.836.94015.5933
41.8524-1.06490.04012.1641-0.17650.5268-0.1397-0.2080.67560.7169-0.038-0.1217-0.28630.07270.17770.285-0.03510.1142-0.1617-0.2381-0.0226103.46169.592525.6994
52.5610.90030.26641.11920.09610.34440.1112-0.27560.37560.1938-0.0837-0.3276-0.1620.112-0.0275-0.12-0.07940.0182-0.15140.09450.1093140.74567.6489-2.1689
67.303-4.9144-0.35922.1134-0.35690-0.2358-0.19040.97210.18230.1694-0.4739-0.1249-0.11940.0664-0.26740.096-0.0218-0.3978-0.12420.7953101.63104.8850.4525
70.989-0.48510.37531.1852-0.13930.62260.08430.23970.5576-0.022-0.1229-0.0421-0.1241-0.04470.0385-0.11190.00730.0755-0.04730.20730.0124119.79759.5804-18.1443
81.0961-0.7063-0.32992.3403-0.45190.3872-0.0039-0.186-0.1212-0.00980.08991.08010.0887-0.4255-0.086-0.2230.00910.1214-0.04750.03720.234667.082943.792910.3863
96.1186-0.44761.49356.2424-0.50343.53010.24890.4289-0.4953-0.3882-0.05940.43740.3177-0.1644-0.1895-0.26160.16750.0489-0.3623-0.14040.245366.177683.2216-5.9178
101.96010.35130.38292.34860.82431.3332-0.10090.35440.4363-0.39420.07080.7013-0.172-0.18620.0301-0.1080.04140.0744-0.13430.0557-0.063475.619651.47681.4308
111.9104-1.18841.05711.9923-1.17741.9991-0.1676-0.55640.54680.7480.12080.6823-0.2341-0.57140.04670.03690.20670.4452-0.0573-0.1690.201869.023167.883926.3752
120.1034-1.0161-0.45620.9942-0.0960.241-0.0001-0.44620.14150.50190.06590.3332-0.0478-0.2137-0.06580.2013-0.03620.1988-0.0124-0.1094-0.164893.460642.228623.4964
132.92760.94551.80514.93871.42445.8391-0.11070.4293-0.0401-1.17130.15980.85090.3025-0.1726-0.04910.2144-0.18750.0448-0.24180.0594-0.417787.969416.6865-0.6591
140.93230.0155-0.08420.855-0.18471.53120.0375-0.00010.16520.28480.00260.06270.0792-0.1103-0.04010.00740.00550.0715-0.12410.0154-0.2564109.35538.49622.2971
151.1923-0.02860.08491.6391-0.08880.5709-0.0212-0.4059-0.18810.64350.0135-0.00380.12340.01470.00770.51510.00550.1270.12580.0906-0.4533111.43816.344436.592
161.52580.45760.44411.7921-0.62184.2172-0.0758-0.0118-0.13590.1970.0205-0.14250.14960.72250.0553-0.13020.15990.0250.2814-0.0838-0.4001137.5930.0481-65.2781
171.9525-0.7136-0.42613.76420.44781.62010.05670.37311.1037-0.56350.00660.0754-0.6672-0.0466-0.0634-0.1334-0.06620.0299-0.37420.44230.4295127.13693.4509-25.193
182.75040.19330.655.9433-0.04073.06230.10470.14420.124-0.0349-0.0775-0.45370.22060.2915-0.0272-0.160.0430.05560.05280.0866-0.2193140.94239.278-19.4497
190.29630.1660.9650.99361.53284.68790.08450.1254-0.30960.13640.0977-0.00720.71280.4499-0.18220.05960.17470.04870.22550.0152-0.2486127.95423.5086-59.497
204.67411.66460.72056.58410.21762.6336-0.1252-0.69480.41680.8263-0.0812-0.9601-0.28280.6940.20640.0171-0.2608-0.47140.0688-0.0132-0.3062152.92253.055537.2253
211.4879-1.0290.53613.0124-1.40480.6032-0.12980.19650.60530.62990.04330.1583-0.2862-0.10030.0865-0.07460.23090.2097-0.3428-0.2920.298376.169499.201314.1333
224.9318-0.3026-0.62330.8333-1.43992.1130.0692-0.64230.02150.7792-0.04210.30.0205-0.1889-0.02710.4345-0.02270.3189-0.00230.0292-0.346491.72325.57637.6133
232.60521.17640.01572.2943-0.21270.1836-0.0908-0.3815-0.31370.6019-0.1811-0.590.4670.5230.27190.23430.1103-0.11840.06680.114-0.318132.80717.634128.5655
240.67731.33010.15290.7748-0.58110.00260.1-0.01140.06180.23530.0451.15810.4814-0.3694-0.1450.3008-0.19450.1036-0.21290.13790.027477.80198.99298.9536
250.7690.6374-0.89285.11572.707500.04190.39740.4404-0.0117-0.1814-0.0613-0.31530.05950.13950.1425-0.08690.02380.1124-0.2214-0.1581106.42555.454910.3782
267.7621-8.23683.96671.6754-3.406300.10490.01340.2534-0.0951-0.07570.2308-0.4211-0.0033-0.02920.18860.1058-0.145-0.01460.11570.312692.367875.6961-22.1816
270.9557-4.9593-0.42411.4853-0.20640-0.0305-0.2594-0.22460.14430.0590.18070.0341-0.0721-0.02850.0687-0.10950.1999-0.1713-0.0225-0.0964100.19142.7082-2.3851
286.5347-3.76770.26050.7028-1.29180.00470.0334-0.03320.3727-0.0442-0.13570.4455-0.2558-0.09990.1023-0.040.3085-0.2073-0.02710.01470.250191.658275.8224-19.9562
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|1 - K|115 }K1 - 115
24X-RAY DIFFRACTION24{ L|25 - L|70 }L25 - 70
25X-RAY DIFFRACTION25{ P|5 - P|19 }P5 - 19
26X-RAY DIFFRACTION26{ T|5 - T|17 }T5 - 17
27X-RAY DIFFRACTION27{ T|18 - T|23 }T18 - 23
28X-RAY DIFFRACTION28{ N|0 - N|13 }N0 - 13

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