7RBP | pdb_00007rbp

Medicago truncatula D-1-piperideine-2-carboxylic acid reductase

PDB DOI: https://doi.org/10.2210/pdb7RBP/pdb

Classification: OXIDOREDUCTASE
Organism(s): Medicago truncatula
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-07-06 Released: 2022-07-06
Deposition Author(s): Torrens-spence, M.P., Weng, J.K.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.272 (Depositor), 0.270 (DCC)
R-Value Work:
0.252 (Depositor), 0.250 (DCC)
R-Value Observed:
0.253 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Pipecolic acid pathway is conserved in systemic acquired resistance between dicotyledon and monocotyledon plants

Torrens-Spence, M.P., Weng, J.K.

To be published.

Macromolecule Content

Total Structure Weight: 72.93 kDa
Atom Count: 4,601
Modeled Residue Count: 594
Deposited Residue Count: 672
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ornithine cyclodeaminase/mu-crystallin	A, B	336	Medicago truncatula	Mutation(s): 0 Gene Names: 11419735, MTR_1g099620
UniProt
Find proteins for B7FJU0 (Medicago truncatula) Explore B7FJU0 Go to UniProtKB: B7FJU0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B7FJU0
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.272 (Depositor), 0.270 (DCC)
R-Value Work: 0.252 (Depositor), 0.250 (DCC)
R-Value Observed: 0.253 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.14	α = 90
b = 83.665	β = 90
c = 113.81	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-07-06

Deposition Author(s):

Torrens-spence, M.P.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2022-07-06
Type: Initial release
Version 1.1: 2023-10-18
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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.