4QJF | pdb_00004qjf

X-ray crystal structure of Thermocuccus kodakarensis RNA polymerase Rpp4/Rpo7 (RpoF/RpoE) complex

PDB DOI: https://doi.org/10.2210/pdb4QJF/pdb

Classification: TRANSCRIPTION
Organism(s): Thermococcus kodakarensis KOD1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-06-03 Released: 2014-10-15
Deposition Author(s): Murakami, K.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free:
0.261 (Depositor), 0.261 (DCC)
R-Value Work:
0.193 (Depositor), 0.196 (DCC)
R-Value Observed:
0.196 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4QJF

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of euryarchaeal RNA polymerase and insight into the evolution of RNA polymerase II structure

(2014) Nat Commun

Macromolecule Content

Total Structure Weight: 36.41 kDa
Atom Count: 2,664
Modeled Residue Count: 308
Deposited Residue Count: 312
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase, subunit E'	A	190	Thermococcus kodakarensis KOD1	Mutation(s): 0 Gene Names: Rpo7, TK1699 EC: 2.7.7.6
UniProt
Find proteins for Q5JIY4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JIY4 Go to UniProtKB: Q5JIY4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JIY4
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase, subunit F	B	122	Thermococcus kodakarensis KOD1	Mutation(s): 0 Gene Names: Rpo4, TK0901 EC: 2.7.7.6
UniProt
Find proteins for Q5JI52 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JI52 Go to UniProtKB: Q5JI52
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JI52
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free: 0.261 (Depositor), 0.261 (DCC)
R-Value Work: 0.193 (Depositor), 0.196 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.465	α = 90
b = 80.942	β = 90
c = 97.413	γ = 90

Software Package:

Software Name	Purpose
Crystal	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-10-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-10-15
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.