6WOX

Thermus thermophilus RNA polymerase initially transcribing complex with 2'dCTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

wwPDB Validation 3D Report Full Report



Literature

The mechanism of discrimination against 2dNTPs by the multisubunit RNA polymerases

Shin, Y.Murakami, K.S.

To be published.

Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alphaA, B315Thermus thermophilusMutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
Find proteins for Q9Z9H6 (Thermus thermophilus)
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Go to UniProtKB:  Q9Z9H6
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit betaC1119Thermus thermophilusMutation(s): 0 
EC: 2.7.7.6
Find proteins for Q8RQE9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'D1505Thermus thermophilusMutation(s): 0 
EC: 2.7.7.6
Find proteins for Q8RQE8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q8RQE8
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omegaE99Thermus thermophilusMutation(s): 0 
Gene Names: rpoZTthAA229_16300TthHC11_16190TTHN1_00070TTMY_2030
EC: 2.7.7.6
Find proteins for A0A1J1EUF1 (Thermus thermophilus)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma factor SigAF423Thermus thermophilusMutation(s): 0 
Find proteins for Q72L95 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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  • Reference Sequence

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Entity ID: 6
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*GP*CP*AP*G)-3')G22Thermus thermophilus

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Entity ID: 7
MoleculeChainsLengthOrganism
DNA (25-MER)H27Thermus thermophilus
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Entity ID: 8
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*CP*A)-3')I3Thermus thermophilus
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DCP
Query on DCP

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D
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O13 P3
RGWHQCVHVJXOKC-SHYZEUOFSA-N
 Ligand Interaction
ZN
Query on ZN

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D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 185.435α = 90
b = 102.654β = 98.914
c = 295.382γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM087350

Revision History 

  • Version 1.0: 2020-06-10
    Type: Initial release