5EJL

MrkH, A novel c-di-GMP dependence transcription regulatory factor.

• PDB DOI: https://doi.org/10.2210/pdb5EJL/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-11-02 Released: 2016-10-19 
• Deposition Author(s): Wang, F., Zhu, D., Gu, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Literature

The PilZ domain of MrkH represents a novel DNA binding motif

Wang, F., He, Q., Su, K., Gao, F., Huang, Y., Lin, Z., Zhu, D., Gu, L.

(2016) Protein Cell 7: 766-772

• PubMed: 27650952 
• DOI: https://doi.org/10.1007/s13238-016-0317-y
• Primary Citation of Related Structures:  
  5EJL

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Organizational Affiliation: 

State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30.73 kDa 
• Atom Count: 2,137 
• Modelled Residue Count: 235 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Klebsiella pneumoniae genome assembly NOVST	A	248	Klebsiella pneumoniae	Mutation(s): 0  Gene Names:  mrkH, AB187_02280, ABY63_13825, KPOL2_01311, KPST15NDM1_03054, PMK1_00755, SE02_15980, SK98_03603, SL05_03385, SL19_03056, SL24_03356, SL48_03379, SL56_02701, SL57_03341, SL69_00334, SL71_01892, SL72_01879, SL84_03450, SL85_03311, SM12_03647, SM17_03206, SM19_03245, SM22_01812, SM40_03226, SM53_03378, SM56_03389, SM59_03130, SM60_03292, SM61_03450, SM63_04027, SM64_03419, SM65_01990, SM67_03796, SM68_03567, SM69_03407, SM70_03107, SM76_03442, SM78_02985, SM80_04811, SM81_03133, SM82_03289, SM83_03401, SM84_02805, SM86_03547, SM88_03405, SM90_03491, SM91_03378, SM92_03536, SM94_03313, SM95_03513, SM96_03441, SM97_03673, SM98_03236, SM99_03225, SN02_03392
UniProt
Find proteins for G3FT00 (Klebsiella pneumoniae) Explore G3FT00  Go to UniProtKB:  G3FT00

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C2E	B [auth A], C [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
SO4	D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.556	α = 90
b = 68.556	β = 90
c = 179.457	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-19 
Deposition Author(s): Wang, F., Zhu, D., Gu, L.

Revision History  

• Version 1.0: 2016-10-19
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations, Structure summary