7VR4 | pdb_00007vr4

Crystal structure of (-)-pulegone reductase PR1294 from Nepeta tenuifolia in complex with NADPH

PDB DOI: https://doi.org/10.2210/pdb7VR4/pdb

Classification: PLANT PROTEIN
Organism(s): Schizonepeta tenuifolia
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-10-21 Released: 2022-10-26
Deposition Author(s): Lin, W., Wang, W.W.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free:
0.196 (Depositor), 0.170 (DCC)
R-Value Work:
0.162 (Depositor), 0.170 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of (-)-pulegone reductase PR1294 from Nepeta tenuifolia in complex with NADPH

Lin, W., Wang, W.W.

To be published.

Macromolecule Content

Total Structure Weight: 38.99 kDa
Atom Count: 2,966
Modeled Residue Count: 340
Deposited Residue Count: 344
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(-)-pulegone reductase PR1294 from Nepeta tenuifolia in complex with NADPH	A	344	Schizonepeta tenuifolia	Mutation(s): 0
UniProt
Find proteins for A0A9X9ZA46 (Schizonepeta tenuifolia) Explore A0A9X9ZA46 Go to UniProtKB: A0A9X9ZA46
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A9X9ZA46
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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free: 0.196 (Depositor), 0.170 (DCC)
R-Value Work: 0.162 (Depositor), 0.170 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.245	α = 90
b = 71.199	β = 101.58
c = 81.146	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-10-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2022-10-26
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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.