6NA4 | pdb_00006na4

Co crystal structure of ECR with Butryl-CoA

PDB DOI: https://doi.org/10.2210/pdb6NA4/pdb

Classification: OXIDOREDUCTASE
Organism(s): Kitasatospora setae KM-6054
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-12-05 Released: 2020-03-18
Deposition Author(s): DeMirci, H.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free:
0.198 (Depositor), 0.198 (DCC)
R-Value Work:
0.170 (Depositor), 0.170 (DCC)
R-Value Observed:
0.170 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6NA4

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Intersubunit Coupling Enables Fast CO2-Fixation by Reductive Carboxylases

DeMirci, H., Rao, Y., Stoffel, G.M., Vogeli, B., Schell, K., Gomez, A., Batyuk, A., Gati, C., Sierra, R.G., Hunter, M.S., Dao, E.H., Ciftci, H.I., Hayes, B., Poitevin, F., Li, P.N., Kaur, M., Tono, K., Saez, D.A., Deutsch, S., Yoshikuni, Y., Grubmuller, H., Erb, T.J., Vohringer-Martinez, E., Wakatsuki, S.

(2022) ACS Cent Sci

DOI: https://doi.org/10.1021/acscentsci.2c00057

Macromolecule Content

Total Structure Weight: 201.83 kDa
Atom Count: 16,313
Modeled Residue Count: 1,786
Deposited Residue Count: 1,792
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative crotonyl-CoA reductase	A, B, C, D	448	Kitasatospora setae KM-6054	Mutation(s): 0 Gene Names: ccr1, KSE_56510
UniProt
Find proteins for E4N096 (Kitasatospora setae (strain ATCC 33774 / DSM 43861 / JCM 3304 / KCC A-0304 / NBRC 14216 / KM-6054)) Explore E4N096 Go to UniProtKB: E4N096
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E4N096
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YAS Query on YAS Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain O [auth D] MOL2 format, chain K [auth C] MOL2 format, chain O [auth D] mmCIF format, chain K [auth C] mmCIF format, chain O [auth D]	K [auth C], O [auth D]	~{S}-[2-[3-[[(2~{R})-4-[[[(2~{S},3~{R},4~{S},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] butanethioate C₂₅ H₄₂ N₇ O₁₇ P₃ S CRFNGMNYKDXRTN-JSFVJHESSA-N		Interactions Focus chain K [auth C] Focus chain O [auth D] Interactions & Density Focus chain K [auth C] Focus chain O [auth D]
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain N [auth D] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain N [auth D] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain N [auth D] mmCIF format, chain H [auth B]	E [auth A], H [auth B], N [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain N [auth D]
2EC (Subject of Investigation/LOI) Query on 2EC Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B]	G [auth A], J [auth B]	9-ETHYL-9H-PURIN-6-YLAMINE C₇ H₉ N₅ MUIPLRMGAXZWSQ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]
VES Query on VES Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D]	F [auth A], I [auth B], L [auth C], P [auth D], Q [auth D]	Pyrrolidine C₄ H₉ N RWRDLPDLKQPQOW-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D] Focus chain Q [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free: 0.198 (Depositor), 0.198 (DCC)
R-Value Work: 0.170 (Depositor), 0.170 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.342	α = 90
b = 78.829	β = 108.06
c = 138.786	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-03-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	NSF-1231306

Revision History (Full details and data files)

Version 1.0: 2020-03-18
Type: Initial release
Version 1.1: 2022-05-11
Changes: Advisory, Database references
Version 1.2: 2024-05-22
Changes: Data collection

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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.