6E8O | pdb_00006e8o

Crystal structure of aryl acid adenylating enzyme FscC from Fuscachelin NRPS in complex with AMP

PDB DOI: https://doi.org/10.2210/pdb6E8O/pdb

Classification: LIGASE
Organism(s): Thermobifida fusca YX
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-07-30 Released: 2019-08-21
Deposition Author(s): Bruner, S.D., Zagulyaeva, A.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.216 (Depositor), 0.216 (DCC)
R-Value Work:
0.189 (Depositor), 0.198 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Implication of MbtH-like proteins in crystallization of the independent NRPS A domains. Crystal structure of FscC: supporting rationale for revised mechanism of freestanding aryl acid adenylating enzymes

Bruner, S.D., Zagulyaeva, A.A.

To be published.

Macromolecule Content

Total Structure Weight: 120.38 kDa
Atom Count: 9,022
Modeled Residue Count: 1,070
Deposited Residue Count: 1,092
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,3-dihydroxybenzoate-AMP ligase	A, B	546	Thermobifida fusca YX	Mutation(s): 0 Gene Names: Tfu_1871
UniProt
Find proteins for Q47NR5 (Thermobifida fusca (strain YX)) Explore Q47NR5 Go to UniProtKB: Q47NR5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q47NR5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.216 (Depositor), 0.216 (DCC)
R-Value Work: 0.189 (Depositor), 0.198 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 207.034	α = 90
b = 51.022	β = 119.87
c = 111.552	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-08-21

Deposition Author(s):

Zagulyaeva, A.A.

Revision History (Full details and data files)

Version 1.0: 2019-08-21
Type: Initial release
Version 1.1: 2019-08-28
Changes: Data collection, Database references, Structure summary
Version 1.2: 2023-10-11
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.