6WF4 | pdb_00006wf4

Crystal Structure of TerC Co-crystallized with Polyporic Acid

PDB DOI: https://doi.org/10.2210/pdb6WF4/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Streptomyces sp. RM-5-8
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2020-04-03 Released: 2021-04-07
Deposition Author(s): Clinger, J.A., Miller, M.D., Hall, R.E., Zhang, Y., Elshahawi, S.I., Thorson, J.S., Van Lanen, S.G., Phillips Jr., G.N., Enzyme Discovery for Natural Product Biosynthesis (NatPro)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free:
0.236 (Depositor), 0.210 (DCC)
R-Value Work:
0.201 (Depositor)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6WF4

Ligand Structure Quality Assessment

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

Literature

Structural and functional characterization of two cooperative enzymes responsible for the stability of p-terphenyls.

Clinger, J.A., Zhang, Y., Liu, Y., Miller, M.D., Hall, R.E., Van Lanen, S.G., Phillips Jr., G.N., Thorson, J.S., Elshahawri, S.I.

To be published.

Macromolecule Content

Total Structure Weight: 20.31 kDa
Atom Count: 1,123
Modeled Residue Count: 130
Deposited Residue Count: 186
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Terfestatin Biosyntheis Enzyme C	A	186	Streptomyces sp. RM-5-8	Mutation(s): 0
UniProt
Find proteins for A0A3B6UEU1 (Streptomyces) Explore A0A3B6UEU1 Go to UniProtKB: A0A3B6UEU1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A3B6UEU1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
U07 (Subject of Investigation/LOI) Query on U07 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]	(2~5~S)-2~3~,2~5~,2~6~-trihydroxy[1~1~,2~1~:2~4~,3~1~-terphenyl]-2~2~(2~5~H)-one C₁₈ H₁₄ O₄ ODPMSLCGNZJREU-HNNXBMFYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
IPA Query on IPA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.236 (Depositor), 0.210 (DCC)
R-Value Work: 0.201 (Depositor)
R-Value Observed: 0.202 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.176	α = 90
b = 97.176	β = 90
c = 29.393	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-04-07

Deposition Author(s):

Elshahawi, S.I.

Van Lanen, S.G.

Phillips Jr., G.N.

Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2021-04-07
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.