1XPP | pdb_00001xpp

Crystal Structure of TA1416,DNA-directed RNA polymerase subunit L, from Thermoplasma acidophilum

• PDB DOI: https://doi.org/10.2210/pdb1XPP/pdb

• Classification: TRANSFERASE
• Organism(s): Thermoplasma acidophilum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-10-09 Released: 2004-11-23 
• Deposition Author(s): Kim, Y., Joachimiak, A., Evdokimova, E., Savchenko, A., Edwards, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.264 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Literature

Crystal structure of TA1416, DNA-directed RNA polymerase subunit L, from Thermoplasma acidophilum

Kim, Y., Joachimiak, A., Evdokimova, E., Savchenko, A., Edwards, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 54.26 kDa 
• Atom Count: 4,060 
• Modeled Residue Count: 397 
• Deposited Residue Count: 460 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit L	A, B, C, D	115	Thermoplasma acidophilum	Mutation(s): 0  Gene Names: rpoL EC: 2.7.7.6
UniProt
Find proteins for Q9HIC5 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore Q9HIC5  Go to UniProtKB:  Q9HIC5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	G [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
SCN	E [auth A], F [auth B], H [auth C]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M
FMT	I [auth C]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.264 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.7	α = 90
b = 69.424	β = 116.77
c = 66.293	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-11-23 
Deposition Author(s): Kim, Y., Joachimiak, A., Evdokimova, E., Savchenko, A., Edwards, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2004-11-23
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2012-09-26
  Changes: Structure summary
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations