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 

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

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: https://doi.org/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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein
A, B, C, D, E
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / 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
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
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
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
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
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
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-11-15
    Changes: Data collection