6EA3 | pdb_00006ea3

Thermobifida fusca FscH adenylation domain complexed with MbtH-like protein FscK and Ser-AMP

PDB DOI: https://doi.org/10.2210/pdb6EA3/pdb

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

Deposited: 2018-08-02 Released: 2019-08-07
Deposition Author(s): Bruner, S.D., Zagulyaeva, A.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.186 (Depositor), 0.190 (DCC)
R-Value Work:
0.165 (Depositor), 0.170 (DCC)
R-Value Observed:
0.166 (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

Comprehensive analysis of protein-protein interactions between MbtH-like protein FscK and adenylation domains in nonribosomal biosynthesis of Fuscachelins.

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

To be published.

Macromolecule Content

Total Structure Weight: 68.77 kDa
Atom Count: 4,155
Modeled Residue Count: 487
Deposited Residue Count: 638
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MbtH-like protein	A	81	Thermobifida fusca YX	Mutation(s): 0 Gene Names: Tfu_1863
UniProt
Find proteins for Q47NS3 (Thermobifida fusca (strain YX)) Explore Q47NS3 Go to UniProtKB: Q47NS3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q47NS3
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
adenylation domain of Fuscachelin synthetase component H	B	557	Thermobifida fusca YX	Mutation(s): 0 Gene Names: Tfu_1866
UniProt
Find proteins for Q47NS0 (Thermobifida fusca (strain YX)) Explore Q47NS0 Go to UniProtKB: Q47NS0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q47NS0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SRP Query on SRP Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	SERYL ADENYLATE C₁₃ H₁₉ N₆ O₉ P UVSYURUCZPPUQD-MACXSXHHSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.186 (Depositor), 0.190 (DCC)
R-Value Work: 0.165 (Depositor), 0.170 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.45	α = 90
b = 68.76	β = 104.81
c = 86.35	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-08-07

Deposition Author(s):

Zagulyaeva, A.A.

Revision History (Full details and data files)

Version 1.0: 2019-08-07
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

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.