3K2G | pdb_00003k2g

Crystal structure of a Resiniferatoxin-binding protein from Rhodobacter sphaeroides

• PDB DOI: https://doi.org/10.2210/pdb3K2G/pdb

• Classification: Resiniferatoxin binding protein
• Organism(s): Cereibacter sphaeroides 2.4.1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-09-30 Released: 2009-10-13 
• Deposition Author(s): Kumaran, D., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.225 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

Crystal structure of a Resiniferatoxin-binding protein from Rhodobacter sphaeroides

Kumaran, D., Burley, S.K., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 5 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 165.05 kDa 
• Atom Count: 11,983 
• Modelled Residue Count: 1,430 
• Deposited Residue Count: 1,456 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Resiniferatoxin-binding, phosphotriesterase-related protein	A, B, C, D	364	Cereibacter sphaeroides 2.4.1	Mutation(s): 0  Gene Names: RHOS4_37320, RHOS4_37320 (RSP_3690), RSP_3690
UniProt
Find proteins for Q3IVY4 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3IVY4  Go to UniProtKB:  Q3IVY4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DTV	H [auth A], K [auth B], N [auth C], Q [auth D]	(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL C4 H10 O2 S2 VHJLVAABSRFDPM-QWWZWVQMSA-N
ZN	E [auth A], F [auth A], I [auth B], J [auth B], L [auth C], M [auth C], O [auth D], P [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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:  0.225 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.735	α = 90
b = 47.414	β = 108.34
c = 188.934	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
SHELXE	model building
ARP/wARP	model building
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-13 
Deposition Author(s): Kumaran, D., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-10-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-12-25
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary