4H7L | pdb_00004h7l

Crystal structure of Plim_4148 protein from Planctomyces limnophilus

• PDB DOI: https://doi.org/10.2210/pdb4H7L/pdb

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


• Deposited: 2012-09-20 Released: 2013-01-02 
• Deposition Author(s): Michalska, K., Bigelow, L., Bruno, C.J.P., Moser, C., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.21 kDa 
• Atom Count: 1,815 
• Modeled Residue Count: 232 
• Deposited Residue Count: 314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein	A, B	157	Planctopirus limnophila DSM 3776	Mutation(s): 0  Gene Names: Plim_4148
UniProt
Find proteins for D5SZ58 (Planctopirus limnophila (strain ATCC 43296 / DSM 3776 / IFAM 1008 / Mu 290)) Explore D5SZ58  Go to UniProtKB:  D5SZ58

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	C [auth A], D [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34H7L

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.091	α = 90
b = 67.091	β = 90
c = 109.874	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELX	model building
MLPHARE	phasing
DM	model building
BUCCANEER	model building
ARP/wARP	model building
Coot	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
DM	phasing
BUCCANEER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-02 
Deposition Author(s): Michalska, K., Bigelow, L., Bruno, C.J.P., Moser, C., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2013-01-02
  Type: Initial release
  
• Version 1.1: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary