4GKG | pdb_00004gkg

Crystal structure of the S-Helix Linker

• PDB DOI: https://doi.org/10.2210/pdb4GKG/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Sinorhizobium meliloti 1021
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-08-11 Released: 2013-08-28 
• Deposition Author(s): Liu, J.W., Lu, D., Sun, Y.J., Wen, J., Yang, Y., Yang, J.G., Wei, X.L., Zhang, X.D., Wang, Y.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.276 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of the S-Helix Linker

Liu, J.W., Lu, D., Sun, Y.J., Wen, J., Yang, Y., Yang, J.G., Wei, X.L., Zhang, X.D., Wang, Y.P.

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)

Macromolecule Content 

• Total Structure Weight: 15.84 kDa 
• Atom Count: 889 
• Modeled Residue Count: 99 
• Deposited Residue Count: 134 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C4-dicarboxylate transport sensor protein dctB	A, B [auth F]	67	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: dctB, RB1524, SMb20612 EC: 2.7.13.3
UniProt
Find proteins for P13633 (Rhizobium meliloti (strain 1021)) Explore P13633  Go to UniProtKB:  P13633

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth A], E [auth F]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.276 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.96	α = 90
b = 40.96	β = 90
c = 302.421	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-28 
Deposition Author(s): Liu, J.W., Lu, D., Sun, Y.J., Wen, J., Yang, Y., Yang, J.G., Wei, X.L., Zhang, X.D., Wang, Y.P.

Revision History  

• Version 1.0: 2013-08-28
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2024-03-13
  Changes: Source and taxonomy
• Version 1.3: 2024-04-03
  Changes: Refinement description