6JUV | pdb_00006juv

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 (Depositor), 0.262 (DCC)
R-Value Work:
0.236 (Depositor), 0.236 (DCC)
R-Value Observed:
0.239 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6JUV

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: 45.69 kDa
Atom Count: 2,966
Modeled Residue Count: 379
Deposited Residue Count: 394
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF 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 (Depositor), 0.262 (DCC)
R-Value Work: 0.236 (Depositor), 0.236 (DCC)
R-Value Observed: 0.239 (Depositor)

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

View more in-depth experimental data

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 is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.