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- PDB-4a3j: RNA Polymerase II initial transcribing complex with a 2nt DNA-RNA... -

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Basic information

Entry
Database: PDB / ID: 4a3j
TitleRNA Polymerase II initial transcribing complex with a 2nt DNA-RNA hybrid and soaked with GMPCPP
Components
  • (DNA-DIRECTED RNA POLYMERASE II SUBUNIT ...Polymerase) x 6
  • (DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC ...RNA polymerase) x 5
  • 5'-D(*AP*GP*CP*TP*AP*GP*CP*TP*TP*TP*CP*BRUP*AP*CP*CP *TP*GP*AP*AP*CP*AP*AP*CP*TP*AP*AP*CP)-3'
  • 5'-D(*GP*TP*AP*GP*AP*AP*AP*GP*CP*TP*AP*GP*CP*TP)-3'
  • 5'-R(*CP*AP)-3'
  • RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7
KeywordsTRANSCRIPTION / TRANSCRIPTION INITIATION
Function / homology
Function and homology information


RPB4-RPB7 complex / : / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / : / 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 ...RPB4-RPB7 complex / : / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / : / 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 / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / RNA polymerase I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / tRNA transcription by RNA polymerase III / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / RNA polymerase II activity / transcription elongation by RNA polymerase I / positive regulation of translational initiation / transcription-coupled nucleotide-excision repair / translesion synthesis / transcription by RNA polymerase I / RNA polymerase I complex / RNA polymerase III complex / transcription by RNA polymerase III / RNA polymerase II, core complex / translation initiation factor binding / transcription elongation by RNA polymerase II / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / peroxisome / cytoplasmic stress granule / single-stranded DNA binding / ribosome biogenesis / single-stranded RNA binding / transcription by RNA polymerase II / 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
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 / 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 / Zinc finger TFIIS-type signature. / 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 / 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 / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / Homeodomain-like / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Single Sheet
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / 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 ...PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / 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
AuthorsCheung, A.C.M. / Sainsbury, S. / Cramer, P.
CitationJournal: Embo J. / Year: 2011
Title: Structural Basis of Initial RNA Polymerase II Transcription.
Authors: Cheung, A.C.M. / Sainsbury, S. / Cramer, P.
History
DepositionSep 30, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references

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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: RPB7, 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
N: 5'-D(*GP*TP*AP*GP*AP*AP*AP*GP*CP*TP*AP*GP*CP*TP)-3'
P: 5'-R(*CP*AP)-3'
T: 5'-D(*AP*GP*CP*TP*AP*GP*CP*TP*TP*TP*CP*BRUP*AP*CP*CP *TP*GP*AP*AP*CP*AP*AP*CP*TP*AP*AP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)528,28125
Polymers527,21315
Non-polymers1,06910
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area88070 Å2
ΔGint-392.5 kcal/mol
Surface area189240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.290, 392.790, 282.660
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 ... , 6 types, 6 molecules ABCDIK

#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: 191664.391 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-1732 / 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
#9: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 / Polymerase / RBP9 / RNA POLYMERASE II SUBUNIT B9 / B12.6 / DNA-DIRECTED RNA POLYMERASE II 14.2 KDA POLYPEPTIDE / ...RBP9 / 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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DNA chain , 2 types, 2 molecules NT

#13: DNA chain 5'-D(*GP*TP*AP*GP*AP*AP*AP*GP*CP*TP*AP*GP*CP*TP)-3' / NON TEMPLATE DNA


Mass: 4328.841 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#15: DNA chain 5'-D(*AP*GP*CP*TP*AP*GP*CP*TP*TP*TP*CP*BRUP*AP*CP*CP *TP*GP*AP*AP*CP*AP*AP*CP*TP*AP*AP*CP)-3' / TEMPLATE DNA


Mass: 8293.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Protein / RNA chain , 2 types, 2 molecules GP

#14: RNA chain 5'-R(*CP*AP)-3' / TRANSCRIPT RNA


Mass: 589.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#7: Protein RPB7, 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

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Non-polymers , 3 types, 10 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-G2P / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-CPP, energy-carrying molecule analogue*YM

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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: 7.04 Å3/Da / Density % sol: 82.39 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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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: 3.7→80 Å / Num. obs: 128404 / % possible obs: 95 % / Observed criterion σ(I): 1.8 / Redundancy: 3.2 % / Biso Wilson estimate: 87.38 Å2 / Rmerge(I) obs: 0.65 / Net I/σ(I): 11.6

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.7→50 Å / Cor.coef. Fo:Fc: 0.9476 / Cor.coef. Fo:Fc free: 0.9275 / SU R Cruickshank DPI: 3.122 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.31 / SU Rfree Blow DPI: 0.346 / SU Rfree Cruickshank DPI: 0.359
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN MG BRU. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=31773. NUMBER WITH APPROX DEFAULT CCP4 ATOM ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN MG BRU. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=31773. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=20. NUMBER TREATED BY BAD NON- BONDED CONTACTS=9.
RfactorNum. reflection% reflectionSelection details
Rfree0.1939 2526 1.97 %RANDOM
Rwork0.1567 ---
obs0.1575 128317 97.35 %-
Displacement parametersBiso mean: 136.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.3662 Å20 Å20 Å2
2--18.9004 Å20 Å2
3----19.2666 Å2
Refine analyzeLuzzati coordinate error obs: 0.831 Å
Refinement stepCycle: LAST / Resolution: 3.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31210 551 41 0 31802
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0132419HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.3543883HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d11624SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes858HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4575HARMONIC5
X-RAY DIFFRACTIONt_it32419HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion24.46
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4274SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance64HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact37907SEMIHARMONIC4
LS refinement shellResolution: 3.7→3.8 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2475 170 1.79 %
Rwork0.2302 9323 -
all0.2305 9493 -
obs--97.35 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.85470.075-2.77351.35271.306800.00760.01650.0301-0.0009-0.02580.0548-0.0387-0.05350.01820.0640.0428-0.049-0.0146-0.0530.050394.432171.8391-19.6822
20.5464-0.00710.01090.5657-0.03520.35510.03450.01280.38130.1146-0.072-0.0587-0.05320.00250.0375-0.1365-0.0060.0538-0.17320.0554-0.0123115.31961.242-6.867
30.5567-0.13330.16990.8015-0.23620.4852-0.0514-0.13290.17220.24370.10460.4086-0.0659-0.2148-0.0533-0.13290.00410.152-0.1569-0.00810.004281.982250.17087.6759
40.37520.0284-0.01490.79650.05280.3773-0.0275-0.2886-0.11310.48320.00690.09650.12240.01560.02060.304-0.00560.08860.0330.0659-0.304110.63516.318336.4169
51.28050.36340.48971.7116-0.60313.3123-0.04460.0276-0.14650.13590.0624-0.02670.12040.4599-0.0178-0.13410.12280.04030.1278-0.0783-0.2591136.66929.8429-65.1683
60.9995-0.5059-0.12735.2745-1.1320.7262-0.05140.14850.5216-0.4065-0.01140.0229-0.33040.05730.0629-0.1625-0.0399-0.0389-0.3040.1520.2784127.09692.8455-25.4396
71.1744-0.32310.22457.3681-0.96372.94310.035-0.08290.19260.0856-0.0203-0.04580.22240.214-0.0147-0.13230.01790.01040.09530.0813-0.1372140.23338.8051-19.5436
81.5301-2.04581.53021.15221.43430-0.0052-0.08920.1401-0.0226-0.0870.1952-0.1114-0.19080.0922-0.0467-0.05730.0228-0.1091-0.06430.122296.366560.7449-13.4929
90.29520.08640.94080.54991.40693.8798-0.05820.0443-0.23050.03870.08640.08720.34790.2706-0.02820.00450.13670.07230.09590.0211-0.1236127.25923.2723-59.5979
106.05531.41142.54122.03590.17880.5523-0.0482-0.38610.17960.23950.0787-0.3383-0.19830.4138-0.03050.055-0.152-0.152-0.0501-0.058-0.2123152.51352.332136.8011
110.8725-1.00930.51781.7641-0.42771.0327-0.06130.14420.50020.5207-0.06060.26930.18390.03870.12190.01250.1520.152-0.2981-0.1450.288476.362399.195313.7002
121.3863-0.9971-1.55790-1.10083.61810.0155-0.1520.04740.19640.01210.12390.05920.0041-0.02760.30340.0040.152-0.10040.0141-0.255191.207125.749237.4636
131.3663-0.24360.61532.164-0.68950.45820.0063-0.076-0.20790.5097-0.1287-0.34570.3850.23110.12230.14830.1087-0.08760.02270.0712-0.2692132.01217.345628.283
140.8312.91040.80300.87291.19180.0129-0.0595-0.04980.10470.00170.33240.1359-0.1484-0.01450.1254-0.1520.087-0.17720.15180.136576.57089.47379.1495
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN N
2X-RAY DIFFRACTION2CHAIN A
3X-RAY DIFFRACTION3CHAIN B
4X-RAY DIFFRACTION4CHAIN C
5X-RAY DIFFRACTION5CHAIN D
6X-RAY DIFFRACTION6CHAIN E
7X-RAY DIFFRACTION7CHAIN F
8X-RAY DIFFRACTION8CHAIN T
9X-RAY DIFFRACTION9CHAIN G
10X-RAY DIFFRACTION10CHAIN H
11X-RAY DIFFRACTION11CHAIN I
12X-RAY DIFFRACTION12CHAIN J
13X-RAY DIFFRACTION13CHAIN K
14X-RAY DIFFRACTION14CHAIN L

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