Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37192.06 
• Atom Count: 2583 
• Residue Count: 322 
• Unique protein chains: 1

2NXF

Crystal Structure of a dimetal phosphatase from Danio rerio LOC 393393

• DOI: 10.2210/pdb2NXF/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Danio rerio
• Expression System: Escherichia coli


• Deposited: 2006-11-17 Released: 2006-12-12 
• Deposition Author(s): Bitto, E., Wesenberg, G.E., Phillips Jr., G.N., McCoy, J.G., Bingman, C.A., Center for Eukaryotic Structural Genomics (CESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.180 
• R-Value Work: 0.161 

Literature

Crystal Structure of a dimetal phosphatase from Danio rerio LOC 393393

Bitto, E., Wesenberg, G.E., Phillips Jr., G.N., McCoy, J.G., Bingman, C.A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Putative dimetal phosphatase	A	322	Danio rerio	Mutation(s): 0  Gene Names: adprm EC: 3.6.1.13, 3.6.1.16, 3.6.1.53
Find proteins for Q7T291 (Danio rerio) Go to UniProtKB:  Q7T291

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EOH	A	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-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: 1.7 Å
• R-Value Free: 0.180 
• R-Value Work: 0.161 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 62.584	α = 90.00
b = 86.593	β = 90.00
c = 157.315	γ = 90.00

Software Package:

Software Name	Purpose
DENZO	data reduction
DM	phasing
PDB_EXTRACT	data extraction
SCALEPACK	data scaling
REFMAC	refinement
HKL-2000	data reduction
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-11-17 
• Released Date: 2006-12-12 
• Deposition Author(s): Bitto, E., Wesenberg, G.E., Phillips Jr., G.N., McCoy, J.G., Bingman, C.A., Center for Eukaryotic Structural Genomics (CESG)

Revision History 

• Version 1.0: 2006-12-12
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Type: Refinement description