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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.289 (Depositor), 0.285 (DCC)
R-Value Work:
0.226 (Depositor), 0.220 (DCC)
R-Value Observed:
0.232 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G3FT00
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C2E Query on C2E Download:Ideal Coordinates CCD File SDF format, chain C [auth D] SDF format, chain D SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain C [auth D] MOL2 format, chain D MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain C [auth D] mmCIF format, chain D mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	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		Interactions Focus chain C [auth D] Focus chain D Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth D] Focus chain D Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.289 (Depositor), 0.285 (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

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Entry History

Deposition Data

Released Date: 2016-08-17

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.