4jkr

X-ray diffraction
4.2Å resolution

Crystal Structure of E. coli RNA Polymerase in complex with ppGpp

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-101170 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
DNA-directed RNA polymerase subunit alpha Chains: A, B, G, H
Molecule details ›
Chains: A, B, G, H
Length: 329 amino acids
Theoretical weight: 36.56 KDa
Source organism: Escherichia coli O104:H4 str. 2009EL-2071
Expression system: Escherichia coli
DNA-directed RNA polymerase subunit beta Chains: C, I
Molecule details ›
Chains: C, I
Length: 1342 amino acids
Theoretical weight: 150.82 KDa
Source organism: Escherichia coli DH1
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A0E0Y7A2 (Residues: 1-1342; Coverage: 100%)
Gene names: O3K_23925, rpoB
Sequence domains:
DNA-DIRECTED RNA POLYMERASE SUBUNIT BETA' Chains: D, J
Molecule details ›
Chains: D, J
Length: 1416 amino acids
Theoretical weight: 156.54 KDa
Source organism: Escherichia coli BW2952
Expression system: Escherichia coli
DNA-directed RNA polymerase subunit omega Chains: E, K
Molecule details ›
Chains: E, K
Length: 90 amino acids
Theoretical weight: 10.12 KDa
Source organism: Escherichia coli DH1
Expression system: Escherichia coli
RNA polymerase sigma factor RpoD Chains: F, L
Molecule details ›
Chains: F, L
Length: 628 amino acids
Theoretical weight: 72.21 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P00579 (Residues: 1-613; Coverage: 100%)
Gene names: JW3039, alt, b3067, rpoD
Sequence domains:

Ligands and Environments

3 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P212121
Unit cell:
a: 187.575Å b: 206.164Å c: 311.062Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.25 0.247 0.318
Expression system: Escherichia coli