5GXE | pdb_00005gxe

Crystal structure of Acryloyl-CoA reductase AcuI in complex with NADPH

PDB DOI: https://doi.org/10.2210/pdb5GXE/pdb

Classification: OXIDOREDUCTASE
Organism(s): Ruegeria pomeroyi DSS-3
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-09-17 Released: 2017-09-20
Deposition Author(s): Zhang, Y.Z., Wang, P., Cao, H.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.198 (Depositor), 0.198 (DCC)
R-Value Work:
0.168 (Depositor), 0.168 (DCC)
R-Value Observed:
0.169 (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 Acryloyl-CoA reductase AcuI in complex with NADPH

Zhang, Y.Z., Wang, P., Cao, H.Y.

To be published.

Macromolecule Content

Total Structure Weight: 70.73 kDa
Atom Count: 5,838
Modeled Residue Count: 662
Deposited Residue Count: 662
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acrylyl-CoA reductase AcuI	A, B	331	Ruegeria pomeroyi DSS-3	Mutation(s): 0 Gene Names: acuI, SPO1914 EC: 1.3.1.84
UniProt
Find proteins for Q5LS56 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LS56 Go to UniProtKB: Q5LS56
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5LS56
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.198 (Depositor), 0.198 (DCC)
R-Value Work: 0.168 (Depositor), 0.168 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.903	α = 90
b = 111.277	β = 90
c = 74.526	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-09-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-09-20
Type: Initial release
Version 1.1: 2023-11-08
Changes: 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.