2ZZW | pdb_00002zzw

Crystal Structure of a Periplasmic Substrate Binding Protein in Complex with Zinc and Lactate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.191 (Depositor), 0.157 (DCC) 
  • R-Value Work: 
    0.151 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 
    0.151 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2ZZW

This is version 2.0 of the entry. See complete history. 

Literature

Crystal structure of a periplasmic substrate-binding protein in complex with calcium lactate

Akiyama, N., Takeda, K., Miki, K.

(2009) J Mol Biology 392: 559-565

  • DOI: https://doi.org/10.1016/j.jmb.2009.07.043
  • Primary Citation Related Structures: 
    2ZZV, 2ZZW, 2ZZX

  • PubMed Abstract: 

    Lactate is utilized in many biological processes, and its transport across biological membranes is mediated with various types of transporters. Here, we report the crystal structures of a lactate-binding protein of a TRAP (tripartite ATP-independent periplasmic) secondary transporter from Thermus thermophilus HB8. The folding of the protein is typical for a type II periplasmic solute-binding protein and forms a dimer in a back-to-back manner. One molecule of l-lactate is clearly identified in a cleft of the protein as a complex with a calcium ion. Detailed crystallographic and biochemical analyses revealed that the calcium ion can be removed from the protein and replaced with other divalent cations. This characterization of the structure of a protein binding with calcium lactate makes a significant contribution to our understanding of the mechanisms by which calcium and lactate are accommodated in cells.

    • Organizational Affiliation: 
    • Department of Chemistry, Kyoto University, Sakyo-ku, Japan.

Macromolecule Content 

  • Total Structure Weight: 81.93 kDa 
  • Atom Count: 5,950 
  • Modeled Residue Count: 660 
  • Deposited Residue Count: 722 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ABC transporter, solute-binding protein
A, B
361Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA0766
UniProt
Find proteins for Q5SK82 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SK82 
Go to UniProtKB:  Q5SK82
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SK82
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.191 (Depositor), 0.157 (DCC) 
  • R-Value Work:  0.151 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 0.151 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.701α = 90
b = 84.986β = 90
c = 113.531γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations