6Y01 | pdb_00006y01

The structure of the molybdenum cofactor binding protein from the phototrophic bacterium Rippkaea orientalis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 
    0.163 (Depositor), 0.163 (DCC) 
  • R-Value Work: 
    0.142 (Depositor), 0.143 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6Y01

This is version 1.1 of the entry. See complete history

Literature

The structure of the Moco carrier protein from Rippkaea orientalis.

Krausze, J.Hercher, T.W.Archna, A.Kruse, T.

(2020) Acta Crystallogr F Struct Biol Commun 76: 453-463

  • DOI: https://doi.org/10.1107/S2053230X20011073
  • Primary Citation Related Structures: 
    6Y01

  • PubMed Abstract: 

    The molybdenum cofactor (Moco) is the prosthetic group of all molybdenum-dependent enzymes except for nitrogenase. The multistep biosynthesis pathway of Moco and its function in molybdenum-dependent enzymes are already well understood. The mechanisms of Moco transfer, storage and insertion, on the other hand, are not. In the cell, Moco is usually not found in its free form and remains bound to proteins because of its sensitivity to oxidation. The green alga Chlamydomonas reinhardtii harbors a Moco carrier protein (MCP) that binds and protects Moco but is devoid of enzymatic function. It has been speculated that this MCP acts as a means of Moco storage and transport. Here, the search for potential MCPs has been extended to the prokaryotes, and many MCPs were found in cyanobacteria. A putative MCP from Rippkaea orientalis (RoMCP) was selected for recombinant production, crystallization and structure determination. RoMCP has a Rossmann-fold topology that is characteristic of nucleotide-binding proteins and a homotetrameric quaternary structure similar to that of the MCP from C. reinhardtii. In each protomer, a positively charged crevice was identified that accommodates up to three chloride ions, hinting at a potential Moco-binding site. Computational docking experiments supported this notion and gave an impression of the RoMCP-Moco complex.


  • Organizational Affiliation
    • Institute of Plant Biology, TU Braunschweig, 38106 Braunschweig, Germany.

Macromolecule Content 

  • Total Structure Weight: 76.07 kDa 
  • Atom Count: 5,248 
  • Modeled Residue Count: 658 
  • Deposited Residue Count: 712 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
p450 cytochrome, putativeA [auth AAA],
B [auth BBB],
C [auth CCC],
D [auth DDD]
178Rippkaea orientalis PCC 8801Mutation(s): 0 
Gene Names: PCC8801_2644
UniProt
Find proteins for B7K4Z0 (Rippkaea orientalis (strain PCC 8801 / RF-1))
Explore B7K4Z0 
Go to UniProtKB:  B7K4Z0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7K4Z0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IMD

Query on IMD



Download:Ideal Coordinates CCD File
E [auth AAA],
I [auth BBB]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
CL

Query on CL



Download:Ideal Coordinates CCD File
F [auth AAA]
G [auth AAA]
H [auth AAA]
J [auth BBB]
K [auth BBB]
F [auth AAA],
G [auth AAA],
H [auth AAA],
J [auth BBB],
K [auth BBB],
L [auth BBB],
M [auth CCC],
N [auth CCC],
O [auth CCC],
P [auth DDD]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free:  0.163 (Depositor), 0.163 (DCC) 
  • R-Value Work:  0.142 (Depositor), 0.143 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.577α = 90
b = 72.044β = 113.333
c = 70.264γ = 90
Software Package:
Software NamePurpose
XDSdata processing
Aimlessdata scaling
PHASERphasing
SHELXEmodel building
Cootmodel building
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2020-09-16 
  • Deposition Author(s): Krausze, J.

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description