4XLZ

N,N'-diacetylchitobiose deacetylase (SeMet derivative) from Pyrococcus furiosus in the presence of cadmium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Multiple crystal forms of N,N'-diacetylchitobiose deacetylase from Pyrococcus furiosus.

Nakamura, T.Niiyama, M.Hashimoto, W.Ida, K.Abe, M.Morita, J.Uegaki, K.

(2015) Acta Crystallogr F Struct Biol Commun 71: 657-662

  • DOI: 10.1107/S2053230X15005695
  • Primary Citation of Related Structures:  
    4XLZ, 4XM0, 4XM1, 4XM2

  • PubMed Abstract: 
  • Native N,N'-diacetylchitobiose deacetylase from Pyrococcus furiosus (Pf-Dac) and its selenomethionine derivative (Se-Pf-Dac) were crystallized and analyzed in the presence and absence of cadmium ion. The four crystal structures fell into three different crystal-packing groups, with the cadmium-free Pf-Dac and Se-Pf-Dac belonging to the same space group, with homologous unit-cell parameters ...

    Native N,N'-diacetylchitobiose deacetylase from Pyrococcus furiosus (Pf-Dac) and its selenomethionine derivative (Se-Pf-Dac) were crystallized and analyzed in the presence and absence of cadmium ion. The four crystal structures fell into three different crystal-packing groups, with the cadmium-free Pf-Dac and Se-Pf-Dac belonging to the same space group, with homologous unit-cell parameters. The crystal structures in the presence of cadmium contained distorted octahedral cadmium complexes coordinated by three chlorides, two O atoms and an S or Se atom from the N-terminal methionine or selenomethionine, respectively. The N-terminal cadmium complex was involved in crystal contacts between symmetry-related molecules through hydrogen bonding to the N-termini. While all six N-termini of Se-Pf-Dac were involved in cadmium-complex formation, only two of the Pf-Dac N-termini participated in complex formation in the Cd-containing crystal, resulting in different crystal forms. These differences are discussed in light of the higher stability of the Cd-Se bond than the Cd-S bond. This work provides an example of the contribution of cadmium towards determining protein crystal quality and packing depending on the use of the native protein or the selenomethionine derivative.


    Organizational Affiliation

    National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka 563-8577, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein
A, B, C, D, E, F
A, B, C, D, E, F
267Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: PF0354
UniProt
Find proteins for Q8U3V1 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U3V1 
Go to UniProtKB:  Q8U3V1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8U3V1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download Ideal Coordinates CCD File 
GC [auth E],
JA [auth B],
NB [auth D],
OB [auth D],
S [auth A],
GC [auth E],
JA [auth B],
NB [auth D],
OB [auth D],
S [auth A],
T [auth A],
TC [auth F],
WA [auth C]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
HEZ
Query on HEZ

Download Ideal Coordinates CCD File 
AC [auth E],
BC [auth E],
CA [auth B],
CC [auth E],
DA [auth B],
AC [auth E],
BC [auth E],
CA [auth B],
CC [auth E],
DA [auth B],
DC [auth E],
EA [auth B],
EB [auth D],
EC [auth E],
FA [auth B],
FB [auth D],
FC [auth E],
GA [auth B],
GB [auth D],
HA [auth B],
HB [auth D],
IA [auth B],
IB [auth D],
JB [auth D],
K [auth A],
KB [auth D],
L [auth A],
LB [auth D],
M [auth A],
MB [auth D],
N [auth A],
NC [auth F],
O [auth A],
OC [auth F],
P [auth A],
PC [auth F],
Q [auth A],
QA [auth C],
QC [auth F],
R [auth A],
RA [auth C],
RC [auth F],
SA [auth C],
SC [auth F],
TA [auth C],
UA [auth C],
VA [auth C],
XB [auth E],
YB [auth E],
ZB [auth E]
HEXANE-1,6-DIOL
C6 H14 O2
XXMIOPMDWAUFGU-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

Download Ideal Coordinates CCD File 
AA [auth B],
AB [auth D],
BA [auth B],
BB [auth D],
CB [auth D],
AA [auth B],
AB [auth D],
BA [auth B],
BB [auth D],
CB [auth D],
DB [auth D],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
LC [auth F],
MC [auth F],
OA [auth C],
PA [auth C],
UB [auth E],
VB [auth E],
WB [auth E],
Z [auth B]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
HC [auth E],
IC [auth E],
JC [auth E],
KA [auth B],
KC [auth E],
HC [auth E],
IC [auth E],
JC [auth E],
KA [auth B],
KC [auth E],
LA [auth B],
MA [auth B],
NA [auth B],
PB [auth D],
QB [auth D],
RB [auth D],
SB [auth D],
TB [auth D],
U [auth A],
UC [auth F],
V [auth A],
VC [auth F],
W [auth A],
WC [auth F],
X [auth A],
XA [auth C],
Y [auth A],
YA [auth C],
ZA [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.895α = 74.69
b = 93.88β = 74.68
c = 93.877γ = 74.68
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and TechnologyJapan24109017

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-10
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy