6VVV

Crystal structure of a Mycobacterium smegmatis transcription initiation complex with Rifampicin-resistant RNA polymerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report



Literature

The antibiotic Sorangicin inhibits DNA unwinding in Rif-resistant mycobacteria

Lilic, M.Chen, J.Boyaci, H.Braffman, N.Hubin, E.A.Darst, S.A.Campbell, E.A.

To be published.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase-binding protein RbpAJ114Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rbpAMSMEG_3858MSMEI_3768
Find proteins for A0QZ11 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QZ11 
Go to UniProtKB:  A0QZ11
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaABT350Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoAMSMEG_1524MSMEI_1488
EC: 2.7.7.6
Find proteins for A0QSL8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QSL8 
Go to UniProtKB:  A0QSL8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC1169Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoBMSMEG_1367MSMEI_1328
EC: 2.7.7.6
Find proteins for P60281 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore P60281 
Go to UniProtKB:  P60281
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'D1317Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoCMSMEG_1368MSMEI_1329
EC: 2.7.7.6
Find proteins for A0QS66 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QS66 
Go to UniProtKB:  A0QS66
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaE107Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoZMSMEG_3053MSMEI_2977
EC: 2.7.7.6
Find proteins for A0QWT1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QWT1 
Go to UniProtKB:  A0QWT1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor SigAF466Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: sigAMSMEG_2758
Find proteins for A0QW02 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QW02 
Go to UniProtKB:  A0QW02
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (31-MER)O31synthetic construct
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsLengthOrganismImage
DNA (26-MER)P26synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
D, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.748α = 90
b = 162.344β = 111.27
c = 137.155γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2020-10-21
    Type: Initial release