7B0E

Crystal structure of SmbA loop deletion mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

High-resolution crystal structure of loop deletion mutant SmbA bound to a monomeric c-di-GMP

Dubey, B.N.Shyp, V.Jenal, U.Schirmer, T.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SmbA291Caulobacter vibrioides CB15Mutation(s): 0 
Gene Names: CC_2504
UniProt
Find proteins for Q9A5E6 (Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15))
Explore Q9A5E6 
Go to UniProtKB:  Q9A5E6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9A5E6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C2E (Subject of Investigation/LOI)
Query on C2E

Download Ideal Coordinates CCD File 
B [auth A]9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
C20 H24 N10 O14 P2
PKFDLKSEZWEFGL-MHARETSRSA-N
EDO
Query on EDO

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C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
Q [auth A],
R [auth A],
S [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
O [auth A],
P [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.04α = 90
b = 56.04β = 90
c = 205.068γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_166652

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-01
    Type: Initial release
  • Version 2.0: 2022-09-07
    Type: Coordinate replacement
    Reason: Occupancy of atoms on special symmetry positions
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2024-01-31
    Changes: Data collection, Refinement description