Biological Assembly 1  

Global Symmetry: Cyclic - C5  (3D View)
Global Stoichiometry: Homo 5-mer - A5 

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

Macromolecule Content

• Total Structure Weight: 72.83 kDa 
• Atom Count: 4,967 
• Modelled Residue Count: 585 
• Deposited Residue Count: 630 
• Unique protein chains: 1

 3HSA

Crystal structure of pleckstrin homology domain (YP_926556.1) from SHEWANELLA AMAZONENSIS SB2B at 1.99 A resolution

• PDB DOI: 10.2210/pdb3HSA/pdb

• Classification: structural genomics, unknown function
• Organism(s): Shewanella amazonensis SB2B
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-06-10 Released: 2009-06-23 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.233 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Literature

Bacterial pleckstrin homology domains: a prokaryotic origin for the PH domain.

Xu, Q., Bateman, A., Finn, R.D., Abdubek, P., Astakhova, T., Axelrod, H.L., Bakolitsa, C., Carlton, D., Chen, C., Chiu, H.J., Chiu, M., Clayton, T., Das, D., Deller, M.C., Duan, L., Ellrott, K., Ernst, D., Farr, C.L., Feuerhelm, J., Grant, J.C., Grzechnik, A., Han, G.W., Jaroszewski, L., Jin, K.K., Klock, H.E., Knuth, M.W., Kozbial, P., Krishna, S.S., Kumar, A., Marciano, D., McMullan, D., Miller, M.D., Morse, A.T., Nigoghossian, E., Nopakun, A., Okach, L., Puckett, C., Reyes, R., Rife, C.L., Sefcovic, N., Tien, H.J., Trame, C.B., van den Bedem, H., Weekes, D., Wooten, T., Hodgson, K.O., Wooley, J., Elsliger, M.A., Deacon, A.M., Godzik, A., Lesley, S.A., Wilson, I.A.

(2010) J Mol Biol 396: 31-46

• PubMed: 19913036 
• DOI: 10.1016/j.jmb.2009.11.006
• Primary Citation of Related Structures:  
  3B77, 3DCX, 3HSA


• PubMed Abstract: 
  

Pleckstrin homology (PH) domains have been identified only in eukaryotic proteins to date. We have determined crystal structures for three members of an uncharacterized protein family (Pfam PF08000), which provide compelling evidence for the existence of PH-like domains in bacteria (PHb). The first two structures contain a single PHb domain that forms a dome-shaped, oligomeric ring with C(5) symmetry. The third structure has an additional helical hairpin attached at the C-terminus and forms a similar but much larger ring with C(12) symmetry. Thus, both molecular assemblies exhibit rare, higher-order, cyclic symmetry but preserve a similar arrangement of their PHb domains, which gives rise to a conserved hydrophilic surface at the intersection of the beta-strands of adjacent protomers that likely mediates protein-protein interactions. As a result of these structures, additional families of PHb domains were identified, suggesting that PH domains are much more widespread than originally anticipated. Thus, rather than being a eukaryotic innovation, the PH domain superfamily appears to have existed before prokaryotes and eukaryotes diverged.

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Organizational Affiliation: 

Joint Center for Structural Genomics, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
pleckstrin homology domain	A, B, C, D, E	126	Shewanella amazonensis SB2B	Mutation(s): 0  Gene Names: Sama_0678, YP_926556.1
UniProt
Find proteins for A1S3D0 (Shewanella amazonensis (strain ATCC BAA-1098 / SB2B)) Explore A1S3D0  Go to UniProtKB:  A1S3D0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	L [auth D], M [auth E]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	F [auth A], G [auth A], H [auth A], I [auth B], J [auth C], K [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	A, B, C, D, E	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS
MSE	A, B, C, D, E	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.233 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data DOI: 10.18430/M33HSA Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.23	α = 90
b = 129.49	β = 90
c = 138.73	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-23 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-06-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2012-10-10
  Changes: Database references
• Version 1.3: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description