1SUM

Crystal structure of a hypothetical protein at 2.0 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1SUM/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-03-26 Released: 2004-08-24 
• Deposition Author(s): Liu, J., Lou, Y., Yokota, H., Adams, P.D., Kim, R., Kim, S.H., Berkeley Structural Genomics Center (BSGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.255 
• R-Value Work: 0.217 
• R-Value Observed: 0.220 

Literature

Crystal structure of a PhoU protein homologue: a new class of metalloprotein containing multinuclear iron clusters.

Liu, J., Lou, Y., Yokota, H., Adams, P.D., Kim, R., Kim, S.H.

(2005) J Biol Chem 280: 15960-15966

• PubMed: 15716271 
• DOI: https://doi.org/10.1074/jbc.M414117200
• Primary Citation of Related Structures:  
  1SUM


• PubMed Abstract: 
  

  PhoU proteins are known to play a role in the regulation of phosphate uptake. In Thermotoga maritima, two PhoU homologues have been identified bioinformatically. Here we report the crystal structure of one of the PhoU homologues at 2.0 A resolution. The structure of the PhoU protein homologue contains a highly symmetric new structural fold composed of two repeats of a three-helix bundle. The structure unexpectedly revealed a trinuclear and a tetranuclear iron cluster that were found to be bound on the surface. Each of the two multinuclear iron clusters is coordinated by a conserved E(D)XXXD motif pair. Our structure reveals a new class of metalloprotein containing multinuclear iron clusters. The possible functional implication based on the structure are discussed.

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Organizational Affiliation: 

Berkeley Structural Genomics Center, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

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,PQS (software)

Macromolecule Content

• Total Structure Weight: 27.5 kDa 
• Atom Count: 1,898 
• Modelled Residue Count: 225 
• Deposited Residue Count: 235 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphate transport system protein phoU homolog 2	A [auth B]	235	Thermotoga maritima	Mutation(s): 0
UniProt
Find proteins for Q9X256 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X256  Go to UniProtKB:  Q9X256

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO3	K [auth B], L [auth B]	PHOSPHITE ION O3 P AQSJGOWTSHOLKH-UHFFFAOYSA-N
NI	I [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
FE	B, C [auth B], D [auth B], E [auth B], F [auth B], G [auth B], H [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA	J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.255 
• R-Value Work: 0.217 
• R-Value Observed: 0.220 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.677	α = 90
b = 90.677	β = 90
c = 45.255	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-24 
Deposition Author(s): Liu, J., Lou, Y., Yokota, H., Adams, P.D., Kim, R., Kim, S.H., Berkeley Structural Genomics Center (BSGC)

Revision History  

• Version 1.0: 2004-08-24
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description