3ROB | pdb_00003rob

The crystal structure of a conserved protein from Planctomyces limnophilus DSM 3776

• PDB DOI: https://doi.org/10.2210/pdb3ROB/pdb

• Classification: Structural Genomics, unknown function
• Organism(s): Planctopirus limnophila DSM 3776
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-04-25 Released: 2011-05-11 
• Deposition Author(s): Tan, K., Li, H., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.194 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Literature

The crystal structure of a conserved protein from Planctomyces limnophilus DSM 3776

Tan, K., Li, H., Bearden, J., Joachimiak, A.

To be published.

Biological Assembly 1  

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

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)

Macromolecule Content 

• Total Structure Weight: 63.74 kDa 
• Atom Count: 4,943 
• Modeled Residue Count: 519 
• Deposited Residue Count: 556 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized conserved protein	A, B, C, D	139	Planctopirus limnophila DSM 3776	Mutation(s): 0  Gene Names: Plim_4131
UniProt
Find proteins for D5SZ41 (Planctopirus limnophila (strain ATCC 43296 / DSM 3776 / IFAM 1008 / Mu 290)) Explore D5SZ41  Go to UniProtKB:  D5SZ41

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth B], G [auth C], H [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.194 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.098	α = 90
b = 68.098	β = 90
c = 124.52	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-11 
Deposition Author(s): Tan, K., Li, H., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2011-05-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary