7BUZ | pdb_00007buz

Crystal structure of Pennisetum glaucum monodehydroascorbate reductase

PDB DOI: https://doi.org/10.2210/pdb7BUZ/pdb

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

Deposited: 2020-04-08 Released: 2021-04-14
Deposition Author(s): Sonkar, K.S., Arulandu, A., Achary, M.M., Reddy, M.K.
Funding Organization(s): Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free:
0.248 (Depositor), 0.208 (DCC)
R-Value Work:
0.187 (Depositor)
R-Value Observed:
0.190 (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 Pennisetum glaucum monodehydroascorbate reductase

Sonkar, K.S., Arulandu, A.

To be published.

Macromolecule Content

Total Structure Weight: 96.58 kDa
Atom Count: 7,219
Modeled Residue Count: 866
Deposited Residue Count: 870
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pennisetum glaucum monodehydroascorbate reductase	A, B	435	Cenchrus americanus	Mutation(s): 0 Gene Names: MDHAR EC: 1.6.5.4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
NAD (Subject of Investigation/LOI) Query on NAD Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.248 (Depositor), 0.208 (DCC)
R-Value Work: 0.187 (Depositor)
R-Value Observed: 0.190 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.572	α = 90
b = 83.46	β = 90
c = 132.872	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
BUSTER	refinement
PDB_EXTRACT	data extraction
PHENIX	model building
BALBES	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-04-14

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: 2021-04-14
Type: Initial release
Version 1.1: 2023-11-29
Changes: Advisory, Data collection, Database references, 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.