5XPB | pdb_00005xpb

Crystal Structure of Selenomethionine labelled Drep4 CIDE domain

PDB DOI: https://doi.org/10.2210/pdb5XPB/pdb

Classification: APOPTOSIS
Organism(s): Drosophila melanogaster
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-06-01 Released: 2018-06-20
Deposition Author(s): Park, H.H., Jeong, J.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.263 (Depositor), 0.290 (DCC)
R-Value Work:
0.216 (Depositor), 0.240 (DCC)
R-Value Observed:
0.219 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Selenomethionine labelled Drep4 CIDE domain

Park, H.H.

To be published.

Macromolecule Content

Total Structure Weight: 113.57 kDa
Atom Count: 6,748
Modeled Residue Count: 860
Deposited Residue Count: 1,000
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNAation factor-related protein 4	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	100	Drosophila melanogaster	Mutation(s): 0 Gene Names: Drep4, Drep-4, drep4, Rep4, CG9414, Dmel_CG9414
UniProt
Find proteins for Q9V3H0 (Drosophila melanogaster) Explore Q9V3H0 Go to UniProtKB: Q9V3H0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9V3H0
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.263 (Depositor), 0.290 (DCC)
R-Value Work: 0.216 (Depositor), 0.240 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.511	α = 102.46
b = 103.722	β = 105.81
c = 103.82	γ = 105.77

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2018-06-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-06-20
Type: Initial release
Version 1.1: 2024-11-20
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.