5O4I

Crystal Structure of mutant M54L/M64L/M96L of Two-Domain Laccase from Streptomyces griseoflavus dialyzed against solution containing 0.25 mM copper sulfate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Incorporation of Copper Ions into T2/T3 Centers of Two-Domain Laccases.

Gabdulkhakov, A.G.Kostareva, O.S.Kolyadenko, I.A.Mikhaylina, A.O.Trubitsina, L.I.Tishchenko, S.V.

(2018) Mol Biol (Mosk) 52: 29-35

  • DOI: https://doi.org/10.7868/S0026898418010056
  • Primary Citation of Related Structures:  
    5O3K, 5O4I, 5O4Q

  • PubMed Abstract: 

    Laccase belongs to the family of copper-containing oxidases. A study was made of the mechanism that sustains the incorporation of copper ions into the T2/T3 centers of recombinant two-domain laccase Streptomyces griseoflavus Ac-993. The occupancy of the T3 center by copper ions was found to increase with an increasing copper content in the culture medium and after dialysis of the protein preparation against a copper sulfate-containing buffer. The T2 center was filled only when overproducer strain cells were grown at a higher copper concentration in the medium. Two-domain laccases were assumed to possess a channel that serves to deliver copper ions to the T3 center during the formation of the three-dimensional laccase conformation and dialysis of the protein preparation. A narrower channel leads to the T2 center in two-domain laccases compared with three-domain ones, rendering the center less accessible for copper atoms. The incorporation of copper ions into the T2 center of two-domain laccases is likely to occur in the course of their biosynthesis or the formation of a functional trimer.


  • Organizational Affiliation

    Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290 Russia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Two-domain laccase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
322Streptomyces griseoflavusMutation(s): 3 
EC: 1.10.3.2
UniProt
Find proteins for A0A0M4FJ81 (Streptomyces griseoflavus)
Explore A0A0M4FJ81 
Go to UniProtKB:  A0A0M4FJ81
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M4FJ81
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
DB [auth F],
FC [auth J],
MB [auth G],
Y [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AB [auth F]
BB [auth F]
BC [auth J]
CA [auth C]
CB [auth F]
AB [auth F],
BB [auth F],
BC [auth J],
CA [auth C],
CB [auth F],
CC [auth J],
DA [auth C],
DC [auth J],
EA [auth C],
EC [auth J],
FA [auth C],
HB [auth G],
IB [auth G],
JA [auth D],
JB [auth G],
JC [auth K],
KA [auth D],
KB [auth G],
KC [auth K],
LA [auth D],
LB [auth G],
LC [auth K],
MA [auth D],
MC [auth K],
NA [auth D],
P [auth A],
Q [auth A],
QB [auth H],
QC [auth L],
RA [auth E],
RB [auth H],
SA [auth E],
TA [auth E],
U [auth B],
UA [auth E],
V [auth B],
VA [auth E],
VB [auth I],
W [auth B],
WA [auth E],
WB [auth I],
X [auth B],
XB [auth I]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU
Query on CU

Download Ideal Coordinates CCD File 
AA [auth C]
AC [auth J]
BA [auth C]
EB [auth G]
FB [auth G]
AA [auth C],
AC [auth J],
BA [auth C],
EB [auth G],
FB [auth G],
GA [auth D],
GB [auth G],
GC [auth K],
HA [auth D],
HC [auth K],
IA [auth D],
IC [auth K],
M [auth A],
N [auth A],
NB [auth H],
NC [auth L],
O [auth A],
OA [auth E],
OB [auth H],
OC [auth L],
PA [auth E],
PB [auth H],
PC [auth L],
QA [auth E],
R [auth B],
S [auth B],
SB [auth I],
T [auth B],
TB [auth I],
UB [auth I],
XA [auth F],
YA [auth F],
YB [auth J],
Z [auth C],
ZA [auth F],
ZB [auth J]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.933α = 90.08
b = 94.931β = 90.2
c = 116.587γ = 91.65
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
RFBRRussian Federation15-04-03002

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 1.1: 2018-04-25
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description