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), 0.167 (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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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.167 (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

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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

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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.