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- PDB-4bbr: Structure of RNA polymerase II-TFIIB complex -

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Basic information

Entry
Database: PDB / ID: 4bbr
TitleStructure of RNA polymerase II-TFIIB complex
Components
  • (DNA-DIRECTED RNA POLYMERASE II SUBUNIT ...Polymerase) x 7
  • (DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC ...RNA polymerase) x 5
  • TRANSCRIPTION INITIATION FACTOR IIB
KeywordsTRANSCRIPTION / RNA POLYMERASE / TFIIB
Function / homology
Function and homology information


RNA polymerase II complex recruiting activity / transcription open complex formation at RNA polymerase II promoter / transcriptional start site selection at RNA polymerase II promoter / RPB4-RPB7 complex / positive regulation of transcription regulatory region DNA binding / : / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / transcription preinitiation complex / RNA Polymerase I Transcription Initiation / : ...RNA polymerase II complex recruiting activity / transcription open complex formation at RNA polymerase II promoter / transcriptional start site selection at RNA polymerase II promoter / RPB4-RPB7 complex / positive regulation of transcription regulatory region DNA binding / : / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / transcription preinitiation complex / RNA Polymerase I Transcription Initiation / : / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / 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 polymerase II general transcription initiation factor activity / 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 II complex binding / 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 / positive regulation of translational initiation / 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 / translation initiation factor binding / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / transcription elongation by RNA polymerase II / P-body / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / peroxisome / cytoplasmic stress granule / single-stranded DNA binding / ribosome biogenesis / transcription by RNA polymerase II / single-stranded RNA binding / nucleic acid binding / protein dimerization activity / nucleotide binding / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Cyclin A; domain 1 - #170 / 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 ...Cyclin A; domain 1 - #170 / 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 / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / Zinc finger, TFIIB-type / TFIIB zinc-binding / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / Cyclin A; domain 1 / 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 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Gyrase A; domain 2 / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Zinc finger TFIIS-type signature. / Cyclin-like superfamily / HRDC-like superfamily / 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 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / 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 / 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 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. / 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
Similarity search - Domain/homology
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 / Transcription initiation factor IIB ...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 / Transcription initiation factor IIB / 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 / OTHER / Resolution: 3.4 Å
AuthorsSainsbury, S. / Niesser, J. / Cramer, P.
CitationJournal: Nature / Year: 2013
Title: Structure and Function of the Initially Transcribing RNA Polymerase II-TFIIB Complex
Authors: Sainsbury, S. / Niesser, J. / Cramer, P.
History
DepositionSep 27, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references
Revision 1.2Jan 30, 2013Group: Database references
Revision 1.3Nov 20, 2019Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AH" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AH" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AK" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BQ" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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 RPABC 1
F: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2
G: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7
H: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3
I: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9
J: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5
K: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11
L: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4
M: TRANSCRIPTION INITIATION FACTOR IIB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)553,05324
Polymers552,41613
Non-polymers63711
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area82680 Å2
ΔGint-448 kcal/mol
Surface area194510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)222.440, 386.760, 254.350
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 / Polymerase / RPB1 / RNA POLYMERASE II SUBUNIT 1 / RNA POLYMERASE II SUBUNIT B1 / DNA-DIRECTED RNA POLYMERASE III ...RPB1 / 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 / Polymerase / 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 / Polymerase / RPB3 / RNA POLYMERASE II SUBUNIT 3 / RNA POLYMERASE II SUBUNIT B3 / B44.5 / DNA-DIRECTED RNA ...RPB3 / 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
#4: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 / Polymerase / 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
#7: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 / Polymerase / 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
#9: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 / Polymerase / RPB9 / RNA POLYMERASE II SUBUNIT B9 / B12.6 / DNA-DIRECTED RNA POLYMERASE II 14.2 KDA POLYPEPTIDE / ...RPB9 / 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
#11: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 / Polymerase / 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

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DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC ... , 5 types, 5 molecules EFHJL

#5: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1 / RNA polymerase / RPB5 / RNA POLYMERASES I\ / II\ / AND III SUBUNIT ABC1 / ABC27 / DNA-DIRECTED RNA POLYMERASES I\ / ...RPB5 / 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
#6: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2 / RNA polymerase / RPB6 / RNA POLYMERASES I\ / II\ / AND III SUBUNIT ABC2 / ABC23 / DNA-DIRECTED RNA POLYMERASES I\ / ...RPB6 / 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
#8: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3 / RNA polymerase / RPB8 / RNA POLYMERASES I\ / II\ / AND III SUBUNIT ABC3 / ABC14.4 / ABC14.5 / DNA-DIRECTED RNA ...RPB8 / 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
#10: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5 / RNA polymerase / RPB10 / RNA POLYMERASES I / II / AND III SUBUNIT ABC5 / ABC10-BETA / ABC8 / DNA-DIRECTED RNA ...RPB10 / 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
#12: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4 / RNA polymerase / RPB12 / 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

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Protein , 1 types, 1 molecules M

#13: Protein TRANSCRIPTION INITIATION FACTOR IIB / TFIIB / GENERAL TRANSCRIPTION FACTOR TFIIB / TRANSCRIPTION FACTOR E


Mass: 38257.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P29055

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Non-polymers , 2 types, 11 molecules

#14: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#15: 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

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Sample preparation

CrystalDensity Matthews: 4.95 Å3/Da / Density % sol: 75.16 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9188
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9188 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 149750 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Biso Wilson estimate: 67.78 Å2 / Rmerge(I) obs: 0.38 / Net I/σ(I): 7.8

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Processing

SoftwareName: BUSTER / Version: 2.11.2 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3.4→49.41 Å / Cor.coef. Fo:Fc: 0.9111 / Cor.coef. Fo:Fc free: 0.8737 / SU R Cruickshank DPI: 0.787 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.67 / SU Rfree Blow DPI: 0.322 / SU Rfree Cruickshank DPI: 0.335
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN MG. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=32789. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN MG. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=32789. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=11.
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2995 2 %RANDOM
Rwork0.1745 ---
obs0.1753 149749 99.96 %-
Displacement parametersBiso mean: 75.56 Å2
Baniso -1Baniso -2Baniso -3
1--15.7464 Å20 Å20 Å2
2--13.2984 Å20 Å2
3---2.4479 Å2
Refine analyzeLuzzati coordinate error obs: 0.582 Å
Refinement stepCycle: LAST / Resolution: 3.4→49.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32789 0 11 0 32800
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0133370HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.3345058HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d12016SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes899HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4776HARMONIC5
X-RAY DIFFRACTIONt_it33370HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.74
X-RAY DIFFRACTIONt_other_torsion24.1
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4415SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance38HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact39268SEMIHARMONIC4
LS refinement shellResolution: 3.4→3.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2904 220 2 %
Rwork0.2341 10778 -
all0.2353 10998 -
obs--99.96 %
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)
16.2858-0.84950.45422.5018-0.15712.82760.05850.1981-0.65450.2529-0.03770.21780.2233-0.2381-0.02080.03250.0548-0.0260.3769-0.0958-0.3942-10.920128.7193-29.9229
22.39350.1807-0.20612.5596-0.19221.69810.02250.40440.5598-0.3014-0.15290.2071-0.3636-0.1450.1304-0.01060.1513-0.08860.36190.0597-0.207-17.990756.2553-34.8445
30.86040.06690.6260.3799-0.17171.61380.03640.0533-0.01850.0173-0.0474-0.10680.10790.24980.0111-0.2321-0.00810.03330.10480.0213-0.325718.98636.453910.9346
40.9183-1.34320.35012.338-0.19570.2295-0.033-0.10280.51620.1667-0.132-0.2131-0.43310.02810.16510.075-0.05080.07010.1145-0.0328-0.172-2.751670.576129.6218
52.03960.61640.17631.0082-0.23690.73040.0609-0.04870.21430.005-0.105-0.1816-0.25660.15660.0441-0.1179-0.07910.01210.10430.1151-0.137433.527165.7074-0.3876
66.5605-3.1459-0.14881.7390.33230.3247-0.1168-0.20790.8002-0.01570.0422-0.1186-0.147-0.20080.07460.03220.0822-0.02980.14260.05120.5142-5.4071103.7722.2905
70.3660.02640.3820.6450.25960.6484-0.0030.15680.3008-0.0736-0.1173-0.0287-0.16470.0120.1202-0.13730.01920.0220.1990.1226-0.199810.636857.2318-13.8443
81.3104-0.22110.18671.19570.07510.44280.0165-0.07390.0029-0.24290.010.5594-0.1358-0.4116-0.0266-0.1230.107-0.10380.45630.02720.0137-44.368744.765513.7066
94.43520.36681.19784.921-0.41373.61860.04210.2131-0.1988-0.46930.09220.10860.35650.0286-0.13430.23860.2609-0.15650.27540.03170.202-40.290981.6697-1.2126
101.73260.56091.00651.06110.59311.6939-0.02320.28190.1712-0.4510.02060.2385-0.0775-0.11760.00260.0010.1087-0.04950.3950.0423-0.1037-33.74249.58967.5961
111.3012-0.6391.13932.2872-1.09322.5081-0.1021-0.35580.41480.42590.08680.3908-0.3639-0.39780.0153-0.00540.20410.07180.4515-0.03420.0367-37.105769.154731.6904
120-0.2839-0.14670.1873-0.51581.1389-0.0519-0.1840.0927-0.00860.06290.0989-0.1746-0.2278-0.011-0.19090.0002-0.03680.1028-0.0767-0.2773-13.003743.244330.3356
132.90890.16522.59111.35330.65684.65960.09980.3588-0.3075-0.46830.03340.20920.22290.0183-0.13320.0433-0.0744-0.06270.156-0.0047-0.2694-18.799816.07598.6999
140.6389-0.04050.07130.2253-0.08911.05650.05910.03750.05220.02430.024-0.00560.1101-0.0766-0.0831-0.19860.0533-0.02760.0149-0.0192-0.32311.376337.98678.6799
150.89210.1870.17390.6264-0.18930.5402-0.0334-0.1303-0.0688-0.065-0.00680.04550.0855-0.030.0402-0.0709-0.02170.00230.22350.0341-0.34455.727918.643644.4981
161.5657-0.00751.06642.3756-0.73994.4492-0.10180.0898-0.0670.08650.1243-0.0945-0.09060.3378-0.0225-0.1051-0.02850.04190.349-0.0181-0.279625.439126.1538-59.573
171.2716-0.43530.0373.49220.31011.98850.1270.34190.6852-0.7489-0.03670.0769-0.77470.0525-0.09030.3683-0.0614-0.00110.35090.31880.301318.051790.5112-23.3626
182.2239-1.1008-0.0555.1265-0.18813.39610.16830.06810.0218-0.0463-0.0823-0.19450.2780.278-0.086-0.27530.0314-0.05270.29660.0214-0.356831.267136.5821-15.0982
190.54270.4890.82580.43521.38542.54580.00250.0615-0.15620.00240.1098-0.00130.21710.1736-0.1123-0.07950.04440.02940.1908-0.0112-0.287616.200519.8922-53.5123
204.62362.80610.08485.0746-0.45992.9148-0.0406-0.14450.12790.19880.1238-0.7894-0.22770.573-0.08320.0555-0.2519-0.25330.47640.0978-0.057347.168154.852939.4466
211.696-0.7428-0.04181.961-0.76150.3175-0.07290.25240.45460.4-0.12770.0553-0.08450.10980.20060.26920.20920.00290.1871-0.10430.3262-30.180199.125816.4808
220-0.8014-0.68561.0531-1.19414.4924-0.0141-0.26810.05970.327-0.01030.08390.0291-0.07190.0244-0.25140.04040.05170.198-0.0212-0.3269-13.858427.943945.8947
232.80240.51060.19641.155-1.31342.9476-0.0413-0.0349-0.0890.2264-0.0406-0.3078-0.03040.29840.082-0.1550.1084-0.0310.081-0.0312-0.323726.662719.114635.1116
244.7742.57723.17580.14561.33273.37920.01650.0254-0.24920.20660.00020.57460.1968-0.2384-0.01660.1769-0.1901-0.07320.28270.17970.1317-29.28129.200118.2894
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 3-81
2X-RAY DIFFRACTION2CHAIN A AND RESID 82-323
3X-RAY DIFFRACTION3CHAIN A AND RESID 324-659
4X-RAY DIFFRACTION4CHAIN A AND RESID 660-831
5X-RAY DIFFRACTION5CHAIN A AND RESID 832-1127
6X-RAY DIFFRACTION6CHAIN A AND RESID 1128-1329
7X-RAY DIFFRACTION7CHAIN A AND RESID 1330-1454
8X-RAY DIFFRACTION8CHAIN B AND RESID 20-234
9X-RAY DIFFRACTION9CHAIN B AND RESID 235-392
10X-RAY DIFFRACTION10CHAIN B AND RESID 393-539
11X-RAY DIFFRACTION11CHAIN B AND RESID 540-735
12X-RAY DIFFRACTION12CHAIN B AND RESID 736-841
13X-RAY DIFFRACTION13CHAIN B AND RESID 842-974
14X-RAY DIFFRACTION14CHAIN B AND RESID 975-1224
15X-RAY DIFFRACTION15CHAIN C AND RESID 3-268
16X-RAY DIFFRACTION16CHAIN D AND RESID 4-221
17X-RAY DIFFRACTION17CHAIN E AND RESID 2-215
18X-RAY DIFFRACTION18CHAIN F AND RESID 72-155
19X-RAY DIFFRACTION19CHAIN G AND RESID 1-171
20X-RAY DIFFRACTION20CHAIN H AND RESID 2-146
21X-RAY DIFFRACTION21CHAIN I AND RESID 2-120
22X-RAY DIFFRACTION22CHAIN J AND RESID 1-65
23X-RAY DIFFRACTION23CHAIN K AND RESID 2-114
24X-RAY DIFFRACTION24CHAIN L AND RESID 27-70

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