8YTQ | pdb_00008ytq

The structure of apoCopC from Thioalkalivibrio paradoxus

PDB DOI: https://doi.org/10.2210/pdb8YTQ/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Thioalkalivibrio paradoxus ARh 1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-26 Released: 2024-04-24
Deposition Author(s): Kulikova, O.G., Solovieva, A.Y., Varfolomeeva, L.A., Dergousova, N.I., Boyko, K.M., Tikhonova, T.V., Popov, V.O.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.231 (Depositor), 0.231 (DCC)
R-Value Work:
0.184 (Depositor), 0.184 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8YTQ

This is version 1.0 of the entry. See complete history.

Literature

The structure of apoCopC from Thioalkalivibrio paradoxus

Kulikova, O.G., Solovieva, A.Y., Varfolomeeva, L.A., Dergousova, N.I., Boyko, K.M., Tikhonova, T.V., Popov, V.O.

To be published.

Macromolecule Content

Total Structure Weight: 56.65 kDa
Atom Count: 4,055
Modeled Residue Count: 509
Deposited Residue Count: 520
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CopC domain-containing protein	A, B, C, D	130	Thioalkalivibrio paradoxus ARh 1	Mutation(s): 0 Gene Names: THITH_13340
UniProt
Find proteins for W0DSL1 (Thioalkalivibrio paradoxus ARh 1) Explore W0DSL1 Go to UniProtKB: W0DSL1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	W0DSL1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth D] SDF format, chain G [auth B] MOL2 format, chain J [auth D] MOL2 format, chain G [auth B] mmCIF format, chain J [auth D] mmCIF format, chain G [auth B]	G [auth B], J [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth B] Focus chain J [auth D] Interactions & Density Focus chain G [auth B] Focus chain J [auth D]
CU (Subject of Investigation/LOI) Query on CU Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain E [auth A]	E [auth A], I [auth C], K [auth D]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth C] Focus chain K [auth D]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain F [auth B] MOL2 format, chain H [auth C] MOL2 format, chain F [auth B] mmCIF format, chain H [auth C] mmCIF format, chain F [auth B]	F [auth B], H [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth B] Focus chain H [auth C] Interactions & Density Focus chain F [auth B] Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.231 (Depositor), 0.231 (DCC)
R-Value Work: 0.184 (Depositor), 0.184 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.084	α = 90
b = 144.787	β = 90.07
c = 55.35	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
MOLREP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-04-24

Deposition Author(s):

Solovieva, A.Y.

Varfolomeeva, L.A.

Dergousova, N.I.

Tikhonova, T.V.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-04-24
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.