4BZ4 | pdb_00004bz4

CorA is a surface-associated copper-binding protein important in Methylomicrobium album BG8 copper acquisition


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.188 (Depositor), 0.197 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 
    0.159 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4BZ4

This is version 1.1 of the entry. See complete history

Literature

Cora is a Copper Repressible Surface-Associated Copper(I)-Binding Protein Produced in Methylomicrobium Album Bg8.

Johnson, K.A.Ve, T.Larsen, O.Pedersen, R.B.Lillehaug, J.R.Jensen, H.B.Helland, R.Karlsen, O.A.

(2014) PLoS One 9: 87750

  • DOI: https://doi.org/10.1371/journal.pone.0087750
  • Primary Citation Related Structures: 
    4BZ4

  • PubMed Abstract: 

    CorA is a copper repressible protein previously identified in the methanotrophic bacterium Methylomicrobium album BG8. In this work, we demonstrate that CorA is located on the cell surface and binds one copper ion per protein molecule, which, based on X-ray Absorption Near Edge Structure analysis, is in the reduced state (Cu(I)). The structure of endogenously expressed CorA was solved using X-ray crystallography. The 1.6 Å three-dimensional structure confirmed the binding of copper and revealed that the copper atom was coordinated in a mononuclear binding site defined by two histidines, one water molecule, and the tryptophan metabolite, kynurenine. This arrangement of the copper-binding site is similar to that of its homologous protein MopE* from Metylococcus capsulatus Bath, confirming the importance of kynurenine for copper binding in these proteins. Our findings show that CorA has an overall fold similar to MopE, including the unique copper(I)-binding site and most of the secondary structure elements. We suggest that CorA plays a role in the M. album BG8 copper acquisition.


  • Organizational Affiliation
    • Norwegian Structural Biology Centre, Faculty of Science, University of Tromsø, Tromsø, Norway.

Macromolecule Content 

  • Total Structure Weight: 155.37 kDa 
  • Atom Count: 10,634 
  • Modeled Residue Count: 1,203 
  • Deposited Residue Count: 1,386 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
COPPER-REPRESSIBLE POLYPEPTIDE
A, B, C, D, E
A, B, C, D, E, F
231Methylomicrobium album BG8Mutation(s): 0 
UniProt
Find proteins for H8GPE3 (Methylomicrobium album BG8)
Explore H8GPE3 
Go to UniProtKB:  H8GPE3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH8GPE3
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P6G

Query on P6G



Download:Ideal Coordinates CCD File
CA [auth E]
DA [auth E]
EA [auth E]
IA [auth F]
J [auth A]
CA [auth E],
DA [auth E],
EA [auth E],
IA [auth F],
J [auth A],
K [auth A],
O [auth B],
P [auth B],
T [auth C],
U [auth C],
Y [auth D]
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
BA [auth E]
HA [auth F]
I [auth A]
N [auth B]
S [auth C]
BA [auth E],
HA [auth F],
I [auth A],
N [auth B],
S [auth C],
X [auth D]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
CU1

Query on CU1



Download:Ideal Coordinates CCD File
FA [auth F]
G [auth A]
L [auth B]
Q [auth C]
V [auth D]
FA [auth F],
G [auth A],
L [auth B],
Q [auth C],
V [auth D],
Z [auth E]
COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
AA [auth E]
GA [auth F]
H [auth A]
M [auth B]
R [auth C]
AA [auth E],
GA [auth F],
H [auth A],
M [auth B],
R [auth C],
W [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KYN
Query on KYN
A, B, C, D, E
A, B, C, D, E, F
L-PEPTIDE LINKINGC10 H12 N2 O3TRP

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.188 (Depositor), 0.197 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 0.159 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.84α = 90
b = 113.17β = 104.51
c = 81.49γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
SOLVEphasing
RESOLVEphasing
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-19
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary