6XN8 | pdb_00006xn8

Crystal Structure of 2-hydroxyacyl CoA lyase (HACL) from Rhodospirillales bacterium URHD0017

PDB DOI: https://doi.org/10.2210/pdb6XN8/pdb

Classification: LYASE
Organism(s): Rhodospirillales bacterium URHD0017
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-07-02 Released: 2021-07-07
Deposition Author(s): Miller, M.D., Xu, W., Olmos Jr., J.L., Chou, A., Clomburg, J.M., Gonzalez, R., Philips Jr., G.N.
Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.212 (Depositor), 0.213 (DCC)
R-Value Work:
0.186 (Depositor), 0.186 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of 2-hydroxyacyl CoA lyase (HACL) from Rhodospirillales bacterium URHD0017

Chou, A., Miller, M.D., Olmos Jr., J.L., Xu, W., Clomburg, J.M., Gonzalez, R., Philips Jr., G.N.

To be published.

Macromolecule Content

Total Structure Weight: 120.05 kDa
Atom Count: 9,544
Modeled Residue Count: 1,079
Deposited Residue Count: 1,104
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-hydroxyacyl-CoA lyase 1	A, B	552	Rhodospirillales bacterium URHD0017	Mutation(s): 0 Gene Names: SAMN02990966_07839
UniProt
Find proteins for A0ACD6BAK1 (Rhodospirillales bacterium URHD0017) Explore A0ACD6BAK1 Go to UniProtKB: A0ACD6BAK1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6BAK1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TZD (Subject of Investigation/LOI) Query on TZD Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], H [auth B]	2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE C₁₂ H₁₈ N₄ O₈ P₂ S ZGJUYGIRPQSCFA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
UNL Query on UNL Download:Ideal Coordinates CCD File	F [auth A], J [auth B]	Unknown ligand JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.212 (Depositor), 0.213 (DCC)
R-Value Work: 0.186 (Depositor), 0.186 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.94	α = 90
b = 64.431	β = 90.88
c = 182.693	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
PHENIX	refinement
ARP/wARP	model building
PHASER	phasing
Aimless	data scaling
DIALS	data reduction
xia2	data reduction
JBluIce-EPICS	data collection

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-07-07

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	STC 1231306
National Science Foundation (NSF, United States)	United States	CBET-1605999
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM115261
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01 CA217255
National Science Foundation (NSF, United States)	United States	GRFP 1450681