4DWZ

Crystal Structure of Ton_0340

PDB DOI: https://doi.org/10.2210/pdb4DWZ/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Thermococcus onnurineus NA1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-02-27 Released: 2013-01-16
Deposition Author(s): Lee, S.G., Lee, K.H., Cha, S.S., Oh, B.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.270
R-Value Work: 0.223

wwPDB Validation 3D Report Full Report

This is version 1.1 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

PubMed: 22948927 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S0907444912024420
Primary Citation of 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: 177.13 kDa
Atom Count: 12,201
Modelled Residue Count: 1,586
Deposited Residue Count: 1,614
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein TON_0340	A, B, C, D, E A, B, C, D, E, F	269	Thermococcus onnurineus NA1	Mutation(s): 0
UniProt
Find proteins for B6YTD8 (Thermococcus onnurineus (strain NA1)) Explore B6YTD8 Go to UniProtKB: B6YTD8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B6YTD8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth E] SDF format, chain EA [auth E] SDF format, chain FA [auth E] SDF format, chain G [auth A] SDF format, chain GA [auth E] SDF format, chain H [auth A] SDF format, chain HA [auth E] SDF format, chain I [auth A] SDF format, chain IA [auth E] SDF format, chain J [auth A] SDF format, chain JA [auth E] SDF format, chain K [auth A] SDF format, chain KA [auth E] SDF format, chain L [auth A] SDF format, chain LA [auth F] SDF format, chain M [auth A] SDF format, chain MA [auth F] SDF format, chain N [auth B] SDF format, chain NA [auth F] SDF format, chain O [auth B] SDF format, chain OA [auth F] SDF format, chain P [auth B] SDF format, chain PA [auth F] SDF format, chain Q [auth B] SDF format, chain QA [auth F] SDF format, chain R [auth B] SDF format, chain RA [auth F] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth E] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain N [auth B] MOL2 format, chain NA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D]	AA [auth D] BA [auth D] CA [auth D] DA [auth E] EA [auth E] AA [auth D], BA [auth D], CA [auth D], DA [auth E], EA [auth E], FA [auth E], G [auth A], GA [auth E], H [auth A], HA [auth E], I [auth A], IA [auth E], J [auth A], JA [auth E], K [auth A], KA [auth E], L [auth A], LA [auth F], M [auth A], MA [auth F], N [auth B], NA [auth F], O [auth B], OA [auth F], P [auth B], PA [auth F], Q [auth B], QA [auth F], R [auth B], RA [auth F], S [auth B], T [auth B], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth D], Z [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain G [auth A] Focus chain GA [auth E] Focus chain H [auth A] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth F] Focus chain M [auth A] Focus chain MA [auth F] Focus chain N [auth B] Focus chain NA [auth F] Focus chain O [auth B] Focus chain OA [auth F] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain R [auth B] Focus chain RA [auth F] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain G [auth A] Focus chain GA [auth E] Focus chain H [auth A] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth F] Focus chain M [auth A] Focus chain MA [auth F] Focus chain N [auth B] Focus chain NA [auth F] Focus chain O [auth B] Focus chain OA [auth F] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain R [auth B] Focus chain RA [auth F] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth D] Focus chain Z [auth D]