6IVH | pdb_00006ivh

Crystal structure of the N-terminal domain of ScpA derived from Thermococcus onnurineus

PDB DOI: https://doi.org/10.2210/pdb6IVH/pdb

Classification: CELL CYCLE
Organism(s): Thermococcus onnurineus NA1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-12-04 Released: 2020-01-22
Deposition Author(s): Jeon, J.-H., Shin, H.-C., Oh, B.-H.
Funding Organization(s): National Research Foundation (Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.259 (Depositor), 0.260 (DCC)
R-Value Work:
0.239 (Depositor), 0.240 (DCC)
R-Value Observed:
0.242 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Archaeal Smc-based condensin lacking kite subunits

Jeon, J.-H., Lee, H.-S., Shin, H.-C., Kwak, M.-J., Kim, Y.-K., Gruber, S., Oh, B.-H.

(2020) IUCrJ

DOI: https://doi.org/10.1107/S2052252519016634

Macromolecule Content

Total Structure Weight: 15.16 kDa
Atom Count: 769
Modeled Residue Count: 94
Deposited Residue Count: 126
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Segregation and condensation protein A	A	126	Thermococcus onnurineus NA1	Mutation(s): 0 Gene Names: TON_1071
UniProt
Find proteins for B6YWU6 (Thermococcus onnurineus (strain NA1)) Explore B6YWU6 Go to UniProtKB: B6YWU6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B6YWU6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.259 (Depositor), 0.260 (DCC)
R-Value Work: 0.239 (Depositor), 0.240 (DCC)
R-Value Observed: 0.242 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.984	α = 90
b = 76.984	β = 90
c = 39.934	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing
RESOLVE	model building
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-01-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	NRF-2018R1A2B3004764

Revision History (Full details and data files)

Version 1.0: 2020-01-22
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Database references, Structure summary

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.