7BTJ | pdb_00007btj

Crystal structure of Pennisetum glaucum monodehydroascorbate reductase in complex with FADH2

PDB DOI: https://doi.org/10.2210/pdb7BTJ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Cenchrus americanus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-04-01 Released: 2021-04-07
Deposition Author(s): Sonkar, K.S., Achary, M.M., Reddy, M.K., Arulandu, A.
Funding Organization(s): Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free:
0.243 (Depositor), 0.230 (DCC)
R-Value Work:
0.186 (Depositor), 0.180 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of Pennisetum glaucum monodehydroascorbate reductase

Sonkar, K.S., Arulandu, A., Achary, M.M., Reddy, M.K.

To be published.

Macromolecule Content

Total Structure Weight: 193.18 kDa
Atom Count: 13,788
Modeled Residue Count: 1,728
Deposited Residue Count: 1,740
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pennisetum glaucum monodehydroascorbate reductase	A, B, C, D	435	Cenchrus americanus	Mutation(s): 0 Gene Names: MDHAR EC: 1.6.5.4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FDA (Subject of Investigation/LOI) Query on FDA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	DIHYDROFLAVINE-ADENINE DINUCLEOTIDE C₂₇ H₃₅ N₉ O₁₅ P₂ YPZRHBJKEMOYQH-UYBVJOGSSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free: 0.243 (Depositor), 0.230 (DCC)
R-Value Work: 0.186 (Depositor), 0.180 (DCC)
R-Value Observed: 0.189 (Depositor)

Diffraction Data: https://doi.org/10.18430/m37btj

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.73	α = 96.39
b = 79.118	β = 97.27
c = 90.687	γ = 111.92

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
ARP/wARP	model building
BALBES	phasing
PHENIX	model building
autoPROC	data reduction
autoPROC	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-04-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	No.BT/PR18774/BIC/101/454/2016

Revision History (Full details and data files)

Version 1.0: 2021-04-07
Type: Initial release
Version 2.0: 2022-09-07
Type: Coordinate replacement
Reason: Ligand identity
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary
Version 2.1: 2023-11-29
Changes: Data collection, Refinement description