7DXO | pdb_00007dxo

The mutant of bifunctional thioesterase catalyzing epimerization and cyclization

PDB DOI: https://doi.org/10.2210/pdb7DXO/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Streptomyces abietis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-01-19 Released: 2022-01-26
Deposition Author(s): Yu, J.H., Song, J., Chi, C.B., Ma, M.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.280 (Depositor), 0.282 (DCC)
R-Value Work:
0.223 (Depositor), 0.226 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Functional Characterization and Crystal Structure of the Bifunctional Thioesterase Catalyzing Epimerization and Cyclization in Skyllamycin Biosynthesis

Yu, J., Juan, S., Chi, C., Liu, T., Geng, T., Cai, Z., Dong, W., Shi, C., Ma, X., Zhang, Z., Ma, X., Xing, B., Jin, H., Zhang, L., Dong, S., Yang, D., Ma, M.

(2021) ACS Catal 11: 11733-11741

DOI: https://doi.org/10.1021/acscatal.1c03064

Macromolecule Content

Total Structure Weight: 90.61 kDa
Atom Count: 6,251
Modeled Residue Count: 792
Deposited Residue Count: 834
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-ribosomal peptide synthetase 4	A, B, C	278	Streptomyces abietis	Mutation(s): 1 Gene Names: nrps4
UniProt
Find proteins for A0ACD6B8Y7 (Streptomyces sp) Explore A0ACD6B8Y7 Go to UniProtKB: A0ACD6B8Y7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B8Y7
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.280 (Depositor), 0.282 (DCC)
R-Value Work: 0.223 (Depositor), 0.226 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.959	α = 90
b = 117.582	β = 90
c = 210.397	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data reduction
CrysalisPro	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-01-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	21877002, 81673332, 81991525, 81573326

Revision History (Full details and data files)

Version 1.0: 2022-01-26
Type: Initial release
Version 1.1: 2022-03-02
Changes: Database references
Version 1.2: 2023-11-29
Changes: Data collection, 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.