2O3O

Crystal Structure of the sensor histidine kinase regulator YycI from Bacillus subtitlis

PDB DOI: https://doi.org/10.2210/pdb2O3O/pdb

Classification: SIGNALING PROTEIN
Organism(s): Bacillus subtilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2006-12-01 Released: 2007-04-10
Deposition Author(s): Santelli, E., Liddington, R.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free: 0.262
R-Value Work: 0.212
R-Value Observed: 0.214

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The Crystal Structure of Bacillus subtilis YycI Reveals a Common Fold for Two Members of an Unusual Class of Sensor Histidine Kinase Regulatory Proteins.

Santelli, E., Liddington, R.C., Mohan, M.A., Hoch, J.A., Szurmant, H.

(2007) J Bacteriol 189: 3290-3295

PubMed: 17307848 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1128/JB.01937-06
Primary Citation of Related Structures:
2O3O

PubMed Abstract:
YycI and YycH are two membrane-anchored periplasmic proteins that regulate the essential Bacillus subtilis YycG histidine kinase through direct interaction. Here we present the crystal structure of YycI at a 2.9-A resolution. YycI forms a dimer, and remarkably the structure resembles that of the two C-terminal domains of YycH despite nearly undetectable sequence homology (10%) between the two proteins.

Organizational Affiliation

Division of Cellular Biology, Mail code MEM-116, Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecule Content

Total Structure Weight: 355.85 kDa
Atom Count: 23,401
Modelled Residue Count: 2,871
Deposited Residue Count: 3,048
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YycI protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	254	Bacillus subtilis	Mutation(s): 6 Gene Names: yycI
UniProt
Find proteins for Q45612 (Bacillus subtilis (strain 168)) Explore Q45612 Go to UniProtKB: Q45612
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q45612
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth D] SDF format, chain O [auth E] SDF format, chain P [auth F] SDF format, chain Q [auth K] SDF format, chain R [auth L] MOL2 format, chain M [auth A] MOL2 format, chain N [auth D] MOL2 format, chain O [auth E] MOL2 format, chain P [auth F] MOL2 format, chain Q [auth K] MOL2 format, chain R [auth L]	M [auth A] N [auth D] O [auth E] P [auth F] Q [auth K] M [auth A], N [auth D], O [auth E], P [auth F], Q [auth K], R [auth L]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth A] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth K] Focus chain R [auth L] Interactions & Density Focus chain M [auth A] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth K] Focus chain R [auth L]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free: 0.262
R-Value Work: 0.212
R-Value Observed: 0.214
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.792	α = 90
b = 161.922	β = 90.9
c = 180.156	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
SHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-04-10

Deposition Author(s):

Santelli, E.

Liddington, R.C.

Revision History (Full details and data files)

Version 1.0: 2007-04-10
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.3: 2023-12-27
Changes: Data collection, Database references, Derived calculations, Refinement description