5YLB | pdb_00005ylb

Crystal structure of Ofd2 from Schizosaccharomyces pombe at 1.80 A

PDB DOI: https://doi.org/10.2210/pdb5YLB/pdb

Classification: OXIDOREDUCTASE
Organism(s): Schizosaccharomyces pombe 972h-
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2017-10-17 Released: 2018-10-24
Deposition Author(s): Wang, J., Gao, Y.X., Guo, G.R., Zhu, Z.L., Teng, M.K., Niu, L.W.
Funding Organization(s): Chinese Ministry of Science and Technology, Chinese National Natural Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.233 (Depositor), 0.253 (DCC)
R-Value Work:
0.185 (Depositor)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Ofd2 from Schizosaccharomyces pombe at 1.80 A

Wang, J., Gao, Y.X., Guo, G.R., Teng, M.K., Niu, L.W.

To be published.

Macromolecule Content

Total Structure Weight: 21.72 kDa
Atom Count: 1,643
Modeled Residue Count: 187
Deposited Residue Count: 187
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein P8A3.02c	A	187	Schizosaccharomyces pombe 972h-	Mutation(s): 0 Gene Names: SPAP8A3.02c
UniProt
Find proteins for Q9UT12 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q9UT12 Go to UniProtKB: Q9UT12
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UT12
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.233 (Depositor), 0.253 (DCC)
R-Value Work: 0.185 (Depositor)
R-Value Observed: 0.188 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.506	α = 90
b = 80.386	β = 90
c = 81.996	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-10-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Chinese Ministry of Science and Technology	China	2012CB917200
Chinese Ministry of Science and Technology	China	2011CBA00800
Chinese National Natural Science Foundation	China	31130018
Chinese National Natural Science Foundation	China	31170726

Revision History (Full details and data files)

Version 1.0: 2018-10-24
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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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.