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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.261
R-Value Work: 0.216
R-Value Observed: 0.218

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1007/s13238-016-0317-y
Primary Citation of Related Structures:
5EJL

Organizational Affiliation

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

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

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(by identity cutoff) | 3D Structure

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... 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G3FT00
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C2E Query on C2E Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	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		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	D [auth A], E [auth A], F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A]	G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
C2E	Binding MOAD: 5EJL	Kd: 240 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.261
R-Value Work: 0.216
R-Value Observed: 0.218
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-10-19

Deposition Author(s):

Wang, F.

Zhu, D.

Gu, L.

Revision History (Full details and data files)

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

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Help and Resources

5EJL

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

The PilZ domain of MrkH represents a novel DNA binding motif

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)