7EOZ

The structure of rice Defective Pollen Wall (DPW) in the complex with its cofactor NADP

PDB DOI: https://doi.org/10.2210/pdb7EOZ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Oryza sativa Japonica Group
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-04-24 Released: 2022-08-24
Deposition Author(s): Yan, L.M., Wang, W., Li, G., Wang, J.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.240
R-Value Work: 0.191
R-Value Observed: 0.194

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Defective Pollen Wall Bridges Lipid and Sugar Metabolisms in Plant Male Reproductive Development

Wang, W., Li, G., Wang, J., Yan, L.M.

To be published.

Macromolecule Content

Total Structure Weight: 117.41 kDa
Atom Count: 7,616
Modelled Residue Count: 955
Deposited Residue Count: 1,064
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acyl-CoA reductase	A, B	532	Oryza sativa Japonica Group	Mutation(s): 0 Gene Names: OSJNBa0091P11.14, Os03g0167600 EC: 1.2.1.84
UniProt
Find proteins for Q8S7T9 (Oryza sativa subsp. japonica) Explore Q8S7T9 Go to UniProtKB: Q8S7T9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8S7T9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP (Subject of Investigation/LOI) Query on NAP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.240
R-Value Work: 0.191
R-Value Observed: 0.194
Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 222.814	α = 90
b = 222.814	β = 90
c = 114.024	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-08-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	China	2017YFC0840300

Revision History (Full details and data files)

Version 1.0: 2022-08-24
Type: Initial release

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 R01GM133198.