Macromolecule Content

Total Structure Weight: 37.19 kDa
Atom Count: 2942
Modelled Residue Count: 314
Deposited Residue Count: 322
Unique protein chains: 1

2NXF

Crystal Structure of a dimetal phosphatase from Danio rerio LOC 393393

PDB DOI: 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.180
R-Value Work: 0.161
R-Value Observed: 0.162

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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:

(by identity cutoff) | 3D Structure

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, adprm, zgc:64213 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7T291
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Ligand Interaction
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction
EOH Query on EOH Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	ETHANOL C₂ H₆ O LFQSCWFLJHTTHZ-UHFFFAOYSA-N		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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
R-Value Work: 0.161
R-Value Observed: 0.162
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

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2006-11-17
Released Date: 2006-12-12

Deposition Author(s):

Wesenberg, G.E.

Phillips Jr., G.N.

Center for Eukaryotic Structural Genomics (CESG)

Revision History (Full details and data files)

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

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.