4OVY | pdb_00004ovy

Crystal structure of Haloacid dehalogenase domain protein hydrolase from Planctomyces limnophilus DSM 3776

• PDB DOI: https://doi.org/10.2210/pdb4OVY/pdb

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


• Deposited: 2014-01-24 Released: 2014-02-05 
• Deposition Author(s): Chang, C., Gu, M., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.175 (Depositor), 0.173 (DCC) 
• R-Value Work: 
  0.131 (Depositor), 0.129 (DCC) 
• R-Value Observed: 
  0.133 (Depositor) 

Literature

Crystal structure of Haloacid dehalogenase domain protein hydrolase from Planctomyces limnophilus DSM 3776

Chang, C., Gu, M., Endres, M., 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)

Macromolecule Content 

• Total Structure Weight: 36.53 kDa 
• Atom Count: 2,774 
• Modeled Residue Count: 305 
• Deposited Residue Count: 310 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloacid dehalogenase domain protein hydrolase	A	310	Planctopirus limnophila DSM 3776	Mutation(s): 0  Gene Names: Plim_1241
UniProt
Find proteins for D5SUM3 (Planctopirus limnophila (strain ATCC 43296 / DSM 3776 / IFAM 1008 / Mu 290)) Explore D5SUM3  Go to UniProtKB:  D5SUM3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	B [auth A], C [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	J [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.175 (Depositor), 0.173 (DCC) 
• R-Value Work:  0.131 (Depositor), 0.129 (DCC) 
• R-Value Observed: 0.133 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.95	α = 90
b = 75.502	β = 90
c = 64.357	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-05 
Deposition Author(s): Chang, C., Gu, M., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2014-02-05
  Type: Initial release
  
• Version 1.1: 2015-02-25
  Changes: Derived calculations
• Version 1.2: 2017-11-22
  Changes: Advisory, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary