4IRM | pdb_00004irm

Crystal structure of mntc r116a mutant exhibits flexibility in the c-terminal domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.305 (Depositor), 0.333 (DCC) 
  • R-Value Work: 
    0.294 (Depositor), 0.320 (DCC) 
  • R-Value Observed: 
    0.294 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history. 

Literature

Arginine 116 stabilizes the entrance to the metal ion-binding site of the MntC protein.

Kanteev, M., Adir, N.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 237-242

  • DOI: https://doi.org/10.1107/S174430911300153X
  • Primary Citation Related Structures: 
    3UJP, 4IRM

  • PubMed Abstract: 

    The cyanobacterium Synechocystis sp. PCC 6803 imports Mn2+ ions via MntCAB, an ABC transport system that is expressed at submicromolar Mn2+ concentrations. The structures of the wild type (WT) and a site-directed mutant of the MntC solute-binding protein have been determined at 2.7 and 3.5 Å resolution, respectively. The WT structure is significantly improved over the previously determined structure (PDB entry 1xvl), showing improved Mn2+ binding site parameters, disulfide bonds in all three monomers and ions bound to the protein surface, revealing the role of Zn2+ ions in the crystallization liquor. The structure of MntC reveals that the active site is surrounded by neutral-to-positive electrostatic potential and is dominated by a network of polar interactions centred around Arg116. The mutation of this residue to alanine was shown to destabilize loops in the entrance to the metal-ion binding site and suggests a possible role in MntC function.

    • Organizational Affiliation: 
    • Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel.

Macromolecule Content 

  • Total Structure Weight: 108.21 kDa 
  • Atom Count: 5,882 
  • Modeled Residue Count: 756 
  • Deposited Residue Count: 990 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Mn transporter; MntC
A, B, C
330Synechocystis sp. PCC 6803Mutation(s): 1 
Gene Names: mntC
UniProt
Find proteins for Q79EF9 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore Q79EF9 
Go to UniProtKB:  Q79EF9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ79EF9
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.305 (Depositor), 0.333 (DCC) 
  • R-Value Work:  0.294 (Depositor), 0.320 (DCC) 
  • R-Value Observed: 0.294 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.4α = 90
b = 128.4β = 90
c = 90.51γ = 120
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-06
    Type: Initial release
  • Version 1.1: 2013-05-01
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary