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- PDB-5c3e: Crystal structure of a transcribing RNA Polymerase II complex rev... -

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Basic information

Entry
Database: PDB / ID: 5c3e
TitleCrystal structure of a transcribing RNA Polymerase II complex reveals a complete transcription bubble
Components
  • (DNA-directed RNA polymerase II subunit ...) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • (Synthetic DNA) x 2
  • Synthetic RNA
KeywordsTRANSFERASE/DNA/RNA / protein-DNA complex / RNA Polyermase II / transcribing complex / 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 / termination of RNA polymerase II transcription ...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 / 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 / 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 initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / DNA-templated transcription initiation / 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 / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / 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 / Gyrase A; domain 2 - #140 ...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 / 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 / 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 / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature.
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 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 / 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 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsBarnes, C.O. / Calero, M. / Malik, I. / Spahr, H. / Zhang, Q. / Pullara, F. / Kaplan, C.D. / Calero, G.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM112686 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM097260 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008424 United States
CitationJournal: Mol.Cell / Year: 2015
Title: Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble.
Authors: Barnes, C.O. / Calero, M. / Malik, I. / Graham, B.W. / Spahr, H. / Lin, G. / Cohen, A.E. / Brown, I.S. / Zhang, Q. / Pullara, F. / Trakselis, M.A. / Kaplan, C.D. / Calero, G.
History
DepositionJun 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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
R: Synthetic RNA
S: Synthetic DNA
U: Synthetic DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)546,38826
Polymers545,75115
Non-polymers63711
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)219.050, 390.940, 278.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II ...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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P08518, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase II subunit RPB3 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P16370
#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 genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPB4, YJL140W, J0654 / Plasmid: pET-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P20433
#7: Protein DNA-directed RNA polymerase II subunit RPB7 / RNA polymerase II subunit B7 / B16


Mass: 20152.207 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: RPB7, YDR404C, D9509.22 / Plasmid: pET-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P34087
#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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P27999
#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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38902

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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 / and III 27 ...RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 kDa polypeptide


Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P20434
#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 / and III 23 ...RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 kDa polypeptide


Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P20435
#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 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P20436
#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 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P22139
#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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40422

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RNA chain , 1 types, 1 molecules R

#13: RNA chain Synthetic RNA


Mass: 2934.831 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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DNA chain , 2 types, 2 molecules SU

#14: DNA chain Synthetic DNA


Mass: 13819.854 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#15: DNA chain Synthetic DNA


Mass: 13766.848 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 11 molecules

#16: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 24.305 Da / Num. of mol.: 2 / 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: 5.53 Å3/Da / Density % sol: 77.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 6000, Ammonium Acetate, Sodium Acetate, DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.4→195.47 Å / Num. all: 145314 / Num. obs: 145314 / % possible obs: 89.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 59.19 Å2 / Rpim(I) all: 0.189 / Rrim(I) all: 0.373 / Rsym value: 0.319 / Net I/av σ(I): 1.896 / Net I/σ(I): 3.2 / Num. measured all: 515843
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
3.4-3.583.21.4130.542222130520.8541.4130.955.4
3.58-3.83.51.1130.663157180600.6511.1131.381.1
3.8-4.063.30.7710.962374189090.4580.7711.890.2
4.06-4.393.30.4641.564588193020.2810.4642.698.6
4.39-4.813.60.3361.965048179850.2010.3363.599.7
4.81-5.383.80.2862.361587163230.1690.2863.999.7
5.38-6.213.80.252.654846144560.1460.254.299.8
6.21-7.63.80.1952.946374122650.1140.1955.199.8
7.6-10.753.80.1453.63605395740.0850.1456.599.7
10.75-90.3633.60.1224.21959453880.0720.1226.799.3

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Processing

Software
NameVersionClassification
BUSTER-TNTBUSTER 2.10.2refinement
SCALA3.3.20data scaling
PDB_EXTRACT3.15data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FKI

3fki


Resolution: 3.7→40 Å / Cor.coef. Fo:Fc: 0.8855 / Cor.coef. Fo:Fc free: 0.8633 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.412
RfactorNum. reflection% reflectionSelection details
Rfree0.2197 3691 3.02 %RANDOM
Rwork0.2006 118525 --
obs0.2012 122114 96.43 %-
Solvent computationBsol: 100.971 Å2
Displacement parametersBiso max: 300 Å2 / Biso mean: 134.22 Å2 / Biso min: 44.9 Å2
Baniso -1Baniso -2Baniso -3
1-9.3655 Å20 Å20 Å2
2--12.4017 Å20 Å2
3----21.7672 Å2
Refine analyzeLuzzati coordinate error obs: 0.53 Å
Refinement stepCycle: final / Resolution: 3.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31475 1033 11 0 32519
Biso mean--102.7 --
Num. residues----4025
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d11903SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes873HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4650HARMONIC5
X-RAY DIFFRACTIONt_it33717HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion4448SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact37640SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d33717HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg45839HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion2
X-RAY DIFFRACTIONt_other_torsion22.66
LS refinement shellResolution: 3.7→3.8 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2866 240 3.13 %
Rwork0.2656 7423 -
all0.2663 7663 -
obs--82.15 %
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)
12.03620.5763-0.56552.99140.13180.0459-0.00980.00440.08020.01240.0022-0.0268-0.01420.03890.0076-0.03890.1520.0412-0.1608-0.06290.123578.642101.037-1.679
20.256-0.2653-0.30320.15230.332300.0019-0.00160.0017-0.00170.0056-0.00310.0062-0.0038-0.00750.01050.01040.010.0039-0.00060.03269.77369.819-1.396
30.0928-0.01760.05280.04730.0370.09450.00040.0056-0.003-0.0024-0.0012-0.00270.00160.00280.00080.0023-0.0065-0.00510.01020.00660.016261.48380.237-19.769
40.2286-0.0075-0.05840.0771-0.12040.1013-0.0001-0.0017-0.0094-0.004-0.001-0.00160.00420.00250.00110.01050.02950.00470.01080.00850.025186.56864.1431.328
50.2825-0.1246-0.03640.5547-0.14560.16070.0149-0.04180.06650.24970.00920.1609-0.0302-0.0162-0.0240.0812-0.01740.1113-0.0845-0.00540.049497.54942.69318.698
60.29850.22270.01660.668-0.03610.18520.03050.11850.3218-0.0117-0.0172-0.0022-0.07980.0686-0.0133-0.0209-0.01840.0088-0.11480.09260.2725130.87573.068-10.555
72.2029-0.19910.1030.19860.33180.33560.00030.05270.043-0.05430.0057-0.03350.02080.0188-0.0060.00210.0710.0817-0.01050.0919-0.0233113.56241.567-31.675
81.07470.08460.19140.54380.01870.4527-0.01350.01910.0620.0211-0.0280.0631-0.0959-0.10970.0415-0.07420.06440.05260.08990.1228-0.001193.07352.815-38.365
92.05140.71050.84491.0411-1.07030.8213-0.0033-0.00110.0029-0.00430.0042-0.01520.00760.027-0.00090.0376-0.0664-0.11520.02390.01270.0469152.15550.95337.092
100.41840.2939-0.42760-1.39440.90430.0024-0.01270.0013-0.008-0.0130.0377-0.00590.01340.01060.09260.02630.10830.0290.0496-0.020890.32725.39638.089
110.8826-0.00811.06310.5895-0.59830.6750.00310.0101-0.02880.0517-0.0092-0.03950.0156-0.00050.00610.03030.0078-0.02070.04510.0411-0.0426130.75816.56628.511
120.42971.0006-0.30870.8551-0.65880.26860.0001-0.0023-0.0036-0.0009-0.01290.0108-0.0024-0.00280.01280.0326-0.02970.00980.00890.00270.053775.41310.13410.023
131.2070.54830.12660.83051.13280.82340.0011-0.0121-0.00630.0086-0.00320.00320.0039-0.00070.00210.025-0.0091-0.00250.0239-0.00680.03794.53587.868-28.313
141.5133-0.56510.24790.3359-0.28710.09710.00070.0121-0.0062-0.0006-0.00020.0127-0.0034-0.0167-0.00050.0235-0.00140.02420.02220.00450.03293.10846.592-6.056
150.69860.71140.18320.59280.1450.2483-0.00050.0116-0.01-0.0244-0.00690.0106-0.0197-0.02560.00740.01040.0180.00440.01820.00090.064246.82449.052-4.749
160.3166-0.0653-0.03850.0636-0.11670.2546-0.0033-0.01070.0197-0.02740.008-0.0037-0.00710.0261-0.00470.00130.015-0.00720.01360.02680.013695.92555.254-13.18
170.06960.04930.02410.14670.03180.11340.00060.0031-0.00470.00040.0027-0.01260.00250.0052-0.00330.04270.0211-0.02310.0351-0.03720.074774.27136.766-14.785
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1142 - A|1274 B|257 - B|325 B|352 - B|400 }A1142 - 1274
2X-RAY DIFFRACTION1{ A|1142 - A|1274 B|257 - B|325 B|352 - B|400 }B257 - 325
3X-RAY DIFFRACTION1{ A|1142 - A|1274 B|257 - B|325 B|352 - B|400 }B352 - 400
4X-RAY DIFFRACTION2{ B|237 - B|256 }B237 - 256
5X-RAY DIFFRACTION3{ B|328 - B|349 }B328 - 349
6X-RAY DIFFRACTION4{ B|501 - B|512 }B501 - 512
7X-RAY DIFFRACTION5{ A|347 - A|808 B|20 - B|61 B|98 - B|121 }A347 - 808
8X-RAY DIFFRACTION5{ A|347 - A|808 B|20 - B|61 B|98 - B|121 }B20 - 61
9X-RAY DIFFRACTION5{ A|347 - A|808 B|20 - B|61 B|98 - B|121 }B98 - 121
10X-RAY DIFFRACTION6{ A|809 - A|1141 A|1275 - A|1394 E|2 - E|215 }A809 - 1141
11X-RAY DIFFRACTION6{ A|809 - A|1141 A|1275 - A|1394 E|2 - E|215 }A1275 - 1394
12X-RAY DIFFRACTION6{ A|809 - A|1141 A|1275 - A|1394 E|2 - E|215 }E2 - 215
13X-RAY DIFFRACTION7{ A|1395 - A|1453 B|1151 - B|1224 }A1395 - 1453
14X-RAY DIFFRACTION7{ A|1395 - A|1453 B|1151 - B|1224 }B1151 - 1224
15X-RAY DIFFRACTION8{ A|2 - A|346 }A2 - 346
16X-RAY DIFFRACTION9{ H|1 - H|146 }H1 - 146
17X-RAY DIFFRACTION10{ J|1 - J|66 J|101 - J|101 }J1 - 66
18X-RAY DIFFRACTION10{ J|1 - J|66 J|101 - J|101 }J101
19X-RAY DIFFRACTION11{ K|1 - K|115 }K1 - 115
20X-RAY DIFFRACTION12{ L|28 - L|70 L|101 - L|101 }L28 - 70
21X-RAY DIFFRACTION12{ L|28 - L|70 L|101 - L|101 }L101
22X-RAY DIFFRACTION13{ S|24 - S|37 U|2 - U|11 }S24 - 37
23X-RAY DIFFRACTION13{ S|24 - S|37 U|2 - U|11 }U2 - 11
26X-RAY DIFFRACTION14{ R|2 - R|10 U|12 - U|26 }R2 - 10
27X-RAY DIFFRACTION14{ R|2 - R|10 U|12 - U|26 }U12 - 26
28X-RAY DIFFRACTION15{ B|62 - B|97 B|122 - B|177 }B62 - 97
29X-RAY DIFFRACTION15{ B|62 - B|97 B|122 - B|177 }B122 - 177
30X-RAY DIFFRACTION16{ A|1801 - A|1804 I|201 - I|202 C|402 - C|402 B|1301 - B|1301 }A1801 - 1804
31X-RAY DIFFRACTION16{ A|1801 - A|1804 I|201 - I|202 C|402 - C|402 B|1301 - B|1301 }I201 - 202
32X-RAY DIFFRACTION16{ A|1801 - A|1804 I|201 - I|202 C|402 - C|402 B|1301 - B|1301 }C402
33X-RAY DIFFRACTION16{ A|1801 - A|1804 I|201 - I|202 C|402 - C|402 B|1301 - B|1301 }B1301
34X-RAY DIFFRACTION17{ U|27 - U|28 }U27 - 28
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.paramCNS_TOPPAR:carbohydrate.top

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