4FC5 | pdb_00004fc5

Crystal Structure of Ton_0340

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.281 (Depositor), 0.281 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4FC5

This is version 1.2 of the entry. See complete history. 

Literature

Experimental phasing using zinc anomalous scattering

Cha, S.S., An, Y.J., Jeong, C.S., Kim, M.K., Lee, S.G., Lee, K.H., Oh, B.H.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1253-1258

  • DOI: https://doi.org/10.1107/S0907444912024420
  • Primary Citation Related Structures: 
    4DT3, 4DWZ, 4FC5

  • PubMed Abstract: 

    Zinc is a suitable metal for anomalous dispersion phasing methods in protein crystallography. Structure determination using zinc anomalous scattering has been almost exclusively limited to proteins with intrinsically bound zinc(s). Here, it is reported that multiple zinc ions can easily be charged onto the surface of proteins with no intrinsic zinc-binding site by using zinc-containing solutions. Zn derivatization of protein surfaces appears to be a largely unnoticed but promising method of protein structure determination.

    • Organizational Affiliation: 
    • Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Ansan 426-744, Republic of Korea. chajung@kordi.re.kr

Macromolecule Content 

  • Total Structure Weight: 178.89 kDa 
  • Atom Count: 13,532 
  • Modeled Residue Count: 1,591 
  • Deposited Residue Count: 1,620 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative uncharacterized protein
A, B, C, D, E
A, B, C, D, E, F
270Thermococcus onnurineus NA1Mutation(s): 0 
Gene Names: TON_0340
UniProt
Find proteins for B6YTD8 (Thermococcus onnurineus (strain NA1))
Explore B6YTD8 
Go to UniProtKB:  B6YTD8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6YTD8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN


Download:Ideal Coordinates CCD File
AA [auth C]
AB [auth F]
BA [auth C]
BB [auth F]
CA [auth C]
AA [auth C],
AB [auth F],
BA [auth C],
BB [auth F],
CA [auth C],
CB [auth F],
DA [auth C],
DB [auth F],
EA [auth C],
EB [auth F],
FA [auth C],
FB [auth F],
G [auth A],
GA [auth C],
GB [auth F],
H [auth A],
HA [auth D],
I [auth A],
IA [auth D],
J [auth A],
JA [auth D],
K [auth A],
KA [auth D],
L [auth A],
LA [auth D],
M [auth A],
MA [auth D],
N [auth A],
NA [auth D],
O [auth B],
OA [auth E],
P [auth B],
PA [auth E],
Q [auth B],
QA [auth E],
R [auth B],
RA [auth E],
S [auth B],
SA [auth E],
T [auth B],
TA [auth E],
U [auth B],
UA [auth E],
V [auth B],
VA [auth E],
W [auth B],
WA [auth E],
X [auth B],
XA [auth E],
Y [auth B],
YA [auth E],
Z [auth C],
ZA [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.281 (Depositor), 0.281 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.181α = 90
b = 107.181β = 90
c = 356.384γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SHARPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-12
    Type: Initial release
  • Version 1.1: 2013-09-04
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations