8J2E | pdb_00008j2e

Structure of the C-terminal subenzyme of the malonyl-CoA reductase from Chloroflexus aurantiacus, mutant N940V/K1106W/S1114R in complex with NADP+ and malonate

PDB DOI: https://doi.org/10.2210/pdb8J2E/pdb

Classification: OXIDOREDUCTASE
Organism(s): Chloroflexus aurantiacus J-10-fl
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-04-14 Released: 2024-04-17
Deposition Author(s): Ma, Q., Liu, C.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.210 (Depositor), 0.209 (DCC)
R-Value Work:
0.188 (Depositor), 0.184 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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Literature

Structures of the C-terminal subenzyme of the malonyl-CoA reductase from Chloroflexus aurantiacus

Ma, Q., Liu, C.

To be published.

Macromolecule Content

Total Structure Weight: 74.61 kDa
Atom Count: 5,265
Modeled Residue Count: 654
Deposited Residue Count: 674
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short-chain dehydrogenase/reductase SDR	A	674	Chloroflexus aurantiacus J-10-fl	Mutation(s): 3 Gene Names: Caur_2614
UniProt
Find proteins for A9WIU3 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl)) Explore A9WIU3 Go to UniProtKB: A9WIU3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A9WIU3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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]
MLA (Subject of Investigation/LOI) Query on MLA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.210 (Depositor), 0.209 (DCC)
R-Value Work: 0.188 (Depositor), 0.184 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.252	α = 90
b = 128.02	β = 103.38
c = 73.87	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-04-17

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2024-04-17
Type: Initial release

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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.