6GTM | pdb_00006gtm

Crystal structure of SmbA in complex with ppGpp.

• PDB DOI: https://doi.org/10.2210/pdb6GTM/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Caulobacter vibrioides CB15
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-06-18 Released: 2019-07-03 
• Deposition Author(s): Dubey, B.N., Schirmer, T.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Reciprocal growth control by competitive binding of nucleotide second messengers to a metabolic switch in Caulobacter crescentus

Shyp, V., Dubey, B.N., Bohm, R., Hartl, J., Nesper, J., Vorholt, J.A., Hiller, S., Schirmer, T., Jenal, U.

(2021) Nat Microbiol 

• DOI: https://doi.org/10.1038/s41564-020-00809-4

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 138.9 kDa 
• Atom Count: 9,096 
• Modeled Residue Count: 1,152 
• Deposited Residue Count: 1,236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SmbA	A, B, C, D	309	Caulobacter vibrioides CB15	Mutation(s): 0  Gene Names: CC_2504
UniProt
Find proteins for A0A0H3C9H2 (Caulobacter vibrioides (strain NA1000 / CB15N)) Explore A0A0H3C9H2  Go to UniProtKB:  A0A0H3C9H2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G4P (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	GUANOSINE-5',3'-TETRAPHOSPHATE C10 H17 N5 O17 P4 BUFLLCUFNHESEH-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.921	α = 90
b = 58.192	β = 93.06
c = 115.253	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-03 
Deposition Author(s): Dubey, B.N., Schirmer, T.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	31003A-166652

Revision History  

• Version 1.0: 2019-07-03
  Type: Initial release
  
• Version 2.0: 2020-07-01
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 3.0: 2020-09-16
  Type: Coordinate replacement
  Reason: Model orientation/position
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Source and taxonomy, Structure summary
• Version 3.1: 2022-07-20
  Changes: Advisory, Database references
• Version 3.2: 2024-01-17
  Changes: Data collection, Refinement description