2NXF | pdb_00002nxf

Crystal Structure of a dimetal phosphatase from Danio rerio LOC 393393

• PDB DOI: https://doi.org/10.2210/pdb2NXF/pdb

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


• 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: 1.70 Å
• R-Value Free: 
  0.180 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

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.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 37.19 kDa 
• Atom Count: 2,942 
• Modeled Residue Count: 314 
• Deposited Residue Count: 322 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative dimetal phosphatase	A	322	Danio rerio	Mutation(s): 3  Gene Names: Dr.12833, LOC 393393 EC: 3.6.1.13 (UniProt), 3.6.1.16 (UniProt), 3.6.1.53 (UniProt)
UniProt
Find proteins for Q7T291 (Danio rerio) Explore Q7T291  Go to UniProtKB:  Q7T291

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	B [auth A], C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EOH	G [auth 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: 1.70 Å
• R-Value Free:  0.180 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.584	α = 90
b = 86.593	β = 90
c = 157.315	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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-11-13
  Changes: Structure summary