6G4G | pdb_00006g4g

Full length ectodomain of ectonucleotide phosphodiesterase/pyrophosphatase-3 (NPP3) including the SMB domains but with a partially disordered active site structure

PDB DOI: https://doi.org/10.2210/pdb6G4G/pdb

Classification: HYDROLASE
Organism(s): Rattus norvegicus
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2018-03-27 Released: 2018-11-07
Deposition Author(s): Dohler, C., Zebisch, M., Strater, N.
Funding Organization(s): German Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.237 (Depositor), 0.251 (DCC)
R-Value Work:
0.196 (Depositor), 0.209 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystallization of ectonucleotide phosphodiesterase/pyrophosphatase-3 and orientation of the SMB domains in the full-length ectodomain.

Dohler, C., Zebisch, M., Krinke, D., Robitzki, A., Strater, N.

(2018) Acta Crystallogr F Struct Biol Commun 74: 696-703

PubMed: 30387774 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2053230X18011111
Primary Citation Related Structures:
6G4G

PubMed Abstract:
Ectonucleotide phosphodiesterase/pyrophosphatase-3 (NPP3, ENPP3) is an ATP-hydrolyzing glycoprotein that is located in the extracellular space. The full-length ectodomain of rat NPP3 was expressed in HEK293S GntI ^- cells, purified using two chromatographic steps and crystallized. Its structure at 2.77 Å resolution reveals that the active-site zinc ions are missing and a large part of the active site and the surrounding residues are flexible. The SMB-like domains have the same orientation in all four molecules in the asymmetric unit. The SMB2 domain is oriented as in NPP2, but the SMB1 domain does not interact with the PDE domain but extends further away from the PDE domain. Deletion of the SMB domains resulted in crystals that diffracted to 2.4 Å resolution and are suitable for substrate-binding studies.

Organizational Affiliation

Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, 04103 Leipzig, Germany.

Macromolecule Content

Total Structure Weight: 387.2 kDa
Atom Count: 24,786
Modeled Residue Count: 3,047
Deposited Residue Count: 3,360
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ectonucleotide pyrophosphatase/phosphodiesterase family member 3	A, B, C, D	840	Rattus norvegicus	Mutation(s): 3 Gene Names: Enpp3, Pdnp3 EC: 3.1.4.1 (PDB Primary Data), 3.6.1.9 (PDB Primary Data), 3.6.1 (UniProt)
UniProt
Find proteins for P97675 (Rattus norvegicus) Explore P97675 Go to UniProtKB: P97675
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P97675
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: P97675-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H, I E, F, G, H, I, J, K	2		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain T [auth C] SDF format, chain Q [auth B] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] MOL2 format, chain R [auth B] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain T [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] mmCIF format, chain R [auth B] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain T [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A]	M [auth A] N [auth A] O [auth A] Q [auth B] R [auth B] M [auth A], N [auth A], O [auth A], Q [auth B], R [auth B], T [auth C], V [auth D], W [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain S [auth C] SDF format, chain P [auth B] SDF format, chain L [auth A] MOL2 format, chain U [auth D] MOL2 format, chain S [auth C] MOL2 format, chain P [auth B] MOL2 format, chain L [auth A] mmCIF format, chain U [auth D] mmCIF format, chain S [auth C] mmCIF format, chain P [auth B] mmCIF format, chain L [auth A]	L [auth A], P [auth B], S [auth C], U [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain U [auth D] Interactions & Density Focus chain L [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain U [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.237 (Depositor), 0.251 (DCC)
R-Value Work: 0.196 (Depositor), 0.209 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.36	α = 86.77
b = 116.3	β = 87.76
c = 124.16	γ = 88.2

Software Package:

Software Name	Purpose
BUSTER	refinement
DIALS	data reduction
STARANISO	data scaling
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-11-07

Deposition Author(s):

Dohler, C.

Zebisch, M.

Strater, N.

Funding Organization	Location	Grant Number
German Research Foundation	Germany	477/13-2

Revision History (Full details and data files)

Version 1.0: 2018-11-07
Type: Initial release
Version 1.1: 2018-11-14
Changes: Data collection, Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-17
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-23
Changes: Structure summary