5KGO | pdb_00005kgo

Structure of K. pneumonia MrkH-c-di-GMP complex

• PDB DOI: https://doi.org/10.2210/pdb5KGO/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-06-13 Released: 2016-08-17 
• Deposition Author(s): Schumacher, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.289 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Literature

To be published: Structures of K. pneumonia MrkH: dual utilization of the PilZ fold for c-di-GMP and DNA binding by a novel activator of biofilm genes

Schumacher, M., Zeng, W.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 57.69 kDa 
• Atom Count: 3,872 
• Modeled Residue Count: 446 
• Deposited Residue Count: 470 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellar brake protein YcgR	A [auth D], B [auth A]	235	Klebsiella pneumoniae	Mutation(s): 2  Gene Names: mrkH, ycgR, AOT21_03001, PMK1_00755
UniProt
Find proteins for G3FT00 (Klebsiella pneumoniae) Explore G3FT00  Go to UniProtKB:  G3FT00

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C2E	C [auth D], D, E [auth A], F [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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.289 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.573	α = 90
b = 74.569	β = 90
c = 135.538	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
RESOLVE	model building
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-17 
Deposition Author(s): Schumacher, M.

Revision History  

• Version 1.0: 2016-08-17
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references, Derived calculations, Structure summary