2HO4 | pdb_00002ho4

Crystal Structure of Protein from Mouse Mm.236127

• PDB DOI: https://doi.org/10.2210/pdb2HO4/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-07-13 Released: 2006-08-15 
• Deposition Author(s): McCoy, J.G., Wesenberg, G.E., Bitto, E., Phillips Jr., G.N., Bingman, C.A., Center for Eukaryotic Structural Genomics (CESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.282 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.248 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Literature

Crystal Structure of Protein from Mouse Mm.236127

McCoy, J.G., WESENBERG, G.E., BITTO, E., PHILLIPS JR., G.N., BINGMAN, C.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 58.59 kDa 
• Atom Count: 4,103 
• Modeled Residue Count: 503 
• Deposited Residue Count: 518 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloacid dehalogenase-like hydrolase domain containing 2	A, B	259	Mus musculus	Mutation(s): 6  Gene Names: Hdhd2
UniProt
Find proteins for Q3UGR5 (Mus musculus) Explore Q3UGR5  Go to UniProtKB:  Q3UGR5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	C [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 2.20 Å
• R-Value Free:  0.282 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.248 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.586	α = 90
b = 68.078	β = 90
c = 190.982	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-15 
Deposition Author(s): McCoy, J.G., Wesenberg, G.E., Bitto, E., Phillips Jr., G.N., Bingman, C.A., Center for Eukaryotic Structural Genomics (CESG)

Revision History  

• Version 1.0: 2006-08-15
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2018-03-14
  Changes: Database references
• Version 1.5: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary