5YL6 | pdb_00005yl6

Crystal structure of Ofd2 in complex with 2OG from Schizosaccharomyces pombe

• PDB DOI: https://doi.org/10.2210/pdb5YL6/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Schizosaccharomyces pombe 972h-
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-10-17 Released: 2019-06-12 
• 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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Ofd2 in complex with 2OG from Schizosaccharomyces pombe

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 21.49 kDa 
• Atom Count: 1,626 
• Modeled Residue Count: 184 
• Deposited Residue Count: 184 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein P8A3.02c	A	184	Schizosaccharomyces pombe 972h-	Mutation(s): 2  Gene Names: SPAP8A3.02c
UniProt
Find proteins for Q9UT12 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q9UT12  Go to UniProtKB:  Q9UT12

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKG	C [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FE	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.114	α = 90
b = 80.312	β = 90
c = 82.607	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-06-12 
Deposition Author(s): Wang, J., Gao, Y.X., Guo, G.R., Zhu, Z.L., Teng, M.K., Niu, L.W.

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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  

• Version 1.0: 2019-06-12
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description