2NP5 | pdb_00002np5

Crystal structure of a transcriptional regulator (RHA1_ro04179) from Rhodococcus sp. Rha1.

• PDB DOI: https://doi.org/10.2210/pdb2NP5/pdb

• Classification: TRANSCRIPTION
• Organism(s): Rhodococcus jostii RHA1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-10-26 Released: 2006-11-28 
• Deposition Author(s): Chruszcz, M., Evdokimova, E., Kagan, O., Cymborowski, M., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.219 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

Crystal structure of a transcriptional regulator (RHA1_ro04179) from Rhodococcus sp. Rha1.

Chruszcz, M., Evdokimova, E., Kagan, O., Cymborowski, M., Savchenko, A., Edwards, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 88.92 kDa 
• Atom Count: 5,881 
• Modeled Residue Count: 716 
• Deposited Residue Count: 812 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator	A, B, C, D	203	Rhodococcus jostii RHA1	Mutation(s): 4  Gene Names: RHA1_ro04179
UniProt
Find proteins for Q0S914 (Rhodococcus jostii (strain RHA1)) Explore Q0S914  Go to UniProtKB:  Q0S914

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LMT	E [auth A], H [auth B]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
NDS	F [auth A], G [auth A], I [auth B]	ETHYL DIMETHYL AMMONIO PROPANE SULFONATE C7 H17 N O3 S NNCRHRDBFDCWPA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.219 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.721	α = 102.31
b = 52.23	β = 107.25
c = 72.853	γ = 89.71

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
Coot	model building
CCP4	phasing
O	model building
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-28 
Deposition Author(s): Chruszcz, M., Evdokimova, E., Kagan, O., Cymborowski, M., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-11-28
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2023-12-27
  Changes: Data collection
• Version 1.5: 2024-10-30
  Changes: Structure summary