6JUV

Crytsal structure of ScpB derived from Pyrococcus yayanosii

PDB DOI: https://doi.org/10.2210/pdb6JUV/pdb

Classification: CELL CYCLE
Organism(s): Pyrococcus yayanosii CH1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-04-15 Released: 2020-01-22
Deposition Author(s): Jeon, J.-H., Lee, H., Oh, B.-H.
Funding Organization(s): National Research Foundation (Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.04 Å
R-Value Free: 0.265
R-Value Work: 0.236
R-Value Observed: 0.239

wwPDB Validation 3D Report Full Report

This is version 1.0 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: 45.69 kDa
Atom Count: 2,966
Modelled Residue Count: 379
Deposited Residue Count: 394
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 B	A, B	197	Pyrococcus yayanosii CH1	Mutation(s): 0 Gene Names: PYCH_12850
UniProt
Find proteins for F8AFC4 (Pyrococcus yayanosii (strain CH1 / JCM 16557)) Explore F8AFC4 Go to UniProtKB: F8AFC4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F8AFC4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B]	C [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.04 Å
R-Value Free: 0.265
R-Value Work: 0.236
R-Value Observed: 0.239
Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.3	α = 90
b = 92.3	β = 90
c = 111.817	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.