4RT5 | pdb_00004rt5

The crystal structure of a glyoxalase/bleomycin resistance protein/dioxygenase protein from planctomyces limnophilus dsm 3776

• PDB DOI: https://doi.org/10.2210/pdb4RT5/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Planctopirus limnophila DSM 3776
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-11-13 Released: 2014-12-03 
• Deposition Author(s): Wu, R., Bearden, J., Kim, Y., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.180 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.151 (Depositor) 
• R-Value Observed: 
  0.153 (Depositor) 

Literature

The crystal structure of a glyoxalase/bleomycin resistance protein/dioxygenase protein from Planctomyces limnophilus dsm 3776

Wu, R., Bearden, J., Kim, Y., Joachimiak, A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 26.03 kDa 
• Atom Count: 1,817 
• Modeled Residue Count: 201 
• Deposited Residue Count: 228 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxalase/bleomycin resistance protein/dioxygenase	A, B	114	Planctopirus limnophila DSM 3776	Mutation(s): 0  Gene Names: Plim_1428 EC: 4.4.1.5
UniProt
Find proteins for D5SVJ2 (Planctopirus limnophila (strain ATCC 43296 / DSM 3776 / IFAM 1008 / Mu 290)) Explore D5SVJ2  Go to UniProtKB:  D5SVJ2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	D [auth A], E [auth A], G [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL	H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI	C [auth A], F [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-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: 1.50 Å
• R-Value Free:  0.180 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.151 (Depositor) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.13	α = 90
b = 77.496	β = 109.19
c = 45.827	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
MLPHARE	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-03 
Deposition Author(s): Wu, R., Bearden, J., Kim, Y., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2014-12-03
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary