2V3Q | pdb_00002v3q

Serendipitous discovery and X-ray structure of a human phosphate binding apolipoprotein

• PDB DOI: https://doi.org/10.2210/pdb2V3Q/pdb
• Entry: 2V3Q supersedes: 2CAP

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2007-06-20 Released: 2008-07-22 
• Deposition Author(s): Morales, R., Berna, A., Carpentier, P., Elias, M., Contreras-Martel, C., Renault, F., Nicodeme, M., Chesne-Seck, M.-L., Bernier, F., Dupuy, J., Schaeffer, C., Diemer, H., Van Dorsselaer, A., Fontecilla, J.C., Masson, P., Rochu, D., Chabriere, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.186 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.127 (Depositor), 0.127 (DCC) 
• R-Value Observed: 
  0.130 (Depositor) 

Literature

Tandem Use of X-Ray Crystallography and Mass Spectrometry to Obtain Ab Initio the Complete and Exact Amino Acids Sequence of Hpbp, a Human 38kDa Apolipoprotein

Diemer, H., Elias, M., Renault, F., Rochu, D., Contreras-Martel, C., Schaeffer, C., Van Dorsselaer, A., Chabriere, E.

(2008) Proteins 71: 1708

• PubMed: 18076037 
• DOI: https://doi.org/10.1002/prot.21866
• Primary Citation Related Structures: 
  2V3Q


• PubMed Abstract: 
  

  The Human Phosphate Binding Protein (HPBP) is a serendipitously discovered apolipoprotein from human plasma that binds phosphate. Amino acid sequence relates HPBP to an intriguing protein family that seems ubiquitous in eukaryotes. These proteins, named DING according to the sequence of their four conserved N-terminal residues, are systematically absent from eukaryotic genome databases. As a consequence, HPBP amino acids sequence had to be first assigned from the electronic density map. Then, an original approach combining X-ray crystallography and mass spectrometry provides the complete and a priori exact sequence of the 38-kDa HPBP. This first complete sequence of a eukaryotic DING protein will be helpful to study HPBP and the entire DING protein family.

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Organizational Affiliation: 
• Laboratoire de Spectrométrie de Masse Bioorganique, Institut Pluridisciplinaire Hubert Curien, UMR 7178 (CNRS-ULP) ECPM, 25 rue Becquerel F67087-Strasbourg-Cedex 2, France.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 39.77 kDa 
• Atom Count: 3,559 
• Modeled Residue Count: 376 
• Deposited Residue Count: 376 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN PHOSPHATE BINDING PROTEIN	A	376	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for P85173 (Unknown prokaryotic organism) Explore P85173  Go to UniProtKB:  P85173

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	B [auth A], C [auth A], E [auth A], P [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], Q [auth A], R [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.186 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.127 (Depositor), 0.127 (DCC) 
• R-Value Observed: 0.130 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.245	α = 90
b = 86.843	β = 90
c = 89.889	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-22 
Deposition Author(s): Morales, R., Berna, A., Carpentier, P., Elias, M., Contreras-Martel, C., Renault, F., Nicodeme, M., Chesne-Seck, M.-L., Bernier, F., Dupuy, J., Schaeffer, C., Diemer, H., Van Dorsselaer, A., Fontecilla, J.C., Masson, P., Rochu, D., Chabriere, E.
• This entry supersedes: 2CAP

Revision History  

• Version 1.0: 2008-07-22
  Type: Initial release
  
• Version 1.1: 2016-01-27
  Changes: Data collection, Derived calculations, Non-polymer description, Other, Version format compliance
• Version 1.2: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary