7VO5 | pdb_00007vo5

Pimaricin type I PKS thioesterase domain (holo Pim TE)

PDB DOI: https://doi.org/10.2210/pdb7VO5/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Streptomyces chattanoogensis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-10-12 Released: 2022-01-19
Deposition Author(s): Bai, L., Zhou, Y.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.232 (Depositor), 0.243 (DCC)
R-Value Work:
0.202 (Depositor), 0.217 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Structural and Mechanistic Insights into Chain Release of the Polyene PKS Thioesterase Domain

Zhou, Y., Tao, W., Qi, Z., Wei, J., Shi, T., Kang, Q., Zheng, J., Zhao, Y., Bai, L.

(2022) ACS Catal 12: 762-776

DOI: https://doi.org/10.1021/acscatal.1c04991

Macromolecule Content

Total Structure Weight: 31.39 kDa
Atom Count: 2,162
Modeled Residue Count: 276
Deposited Residue Count: 286
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ScnS4	A	286	Streptomyces chattanoogensis	Mutation(s): 0 Gene Names: scnS4
UniProt
Find proteins for F1CLA7 (Streptomyces chattanoogensis) Explore F1CLA7 Go to UniProtKB: F1CLA7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F1CLA7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
81E (Subject of Investigation/LOI) Query on 81E Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(1R,3S,5E,7S,11R,13E,15E,17E,19E,21R,23S,24R,25S)-11,24-dimethyl-1,3,7,21,25-pentakis(oxidanyl)-10,27-dioxabicyclo[21.3.1]heptacosa-5,13,15,17,19-pentaen-9-one C₂₇ H₄₀ O₈ HPNUEFYWFLZIDL-RYQDMBGZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.232 (Depositor), 0.243 (DCC)
R-Value Work: 0.202 (Depositor), 0.217 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.449	α = 90
b = 95.449	β = 90
c = 102.708	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-01-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded	China	--

Revision History (Full details and data files)

Version 1.0: 2022-01-19
Type: Initial release
Version 1.1: 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.