3M05 | pdb_00003m05

The crystal structure of a functionally unknown protein PEPE_1480 from Pediococcus pentosaceus ATCC 25745

• PDB DOI: https://doi.org/10.2210/pdb3M05/pdb

• Classification: structural genomics, unknown function
• Organism(s): Pediococcus pentosaceus ATCC 25745
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-03-02 Released: 2010-03-16 
• Deposition Author(s): Tan, K., Bigelow, L., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 
  0.247 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Literature

The crystal structure of a functionally unknown protein PEPE_1480 from Pediococcus pentosaceus ATCC 25745

Tan, K., Bigelow, L., Bearden, J., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 39.11 kDa 
• Atom Count: 2,352 
• Modeled Residue Count: 298 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein PEPE_1480	A, B, C	114	Pediococcus pentosaceus ATCC 25745	Mutation(s): 0  Gene Names: PEPE_1480
UniProt
Find proteins for Q03E61 (Pediococcus pentosaceus (strain ATCC 25745 / CCUG 21536 / LMG 10740 / 183-1w)) Explore Q03E61  Go to UniProtKB:  Q03E61

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth B], G [auth C], H [auth C], I [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free:  0.247 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.774	α = 90
b = 119.774	β = 90
c = 119.349	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
RESOLVE	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-16 
Deposition Author(s): Tan, K., Bigelow, L., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-04-09
  Changes: Data collection
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary