8KI5

PhmA, a type I diterpene synthase without NST/DTE motif

PDB DOI: https://doi.org/10.2210/pdb8KI5/pdb

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

Deposited: 2023-08-22 Released: 2023-10-04
Deposition Author(s): Zhang, B., Ge, H.M., Zhu, A., Zhang, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC), Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.223
R-Value Work: 0.182
R-Value Observed: 0.186

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Biosynthesis of Platelet Activating Factor Antagonist Phomactins Revealing a New Class of Type I Diterpene Synthase

Zhang, L., Zhang, B., Zhu, A., Liu, S.H., Wu, R., Zhang, X., Xu, Z.R., Ge, H.M.

To be published.

Macromolecule Content

Total Structure Weight: 37.71 kDa
Atom Count: 2,393
Modelled Residue Count: 284
Deposited Residue Count: 332
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PhmA	A	332	Phoma	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FOH (Subject of Investigation/LOI) Query on FOH Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	(2Z,6Z)-3,7,11-trimethyldodeca-2,6,10-trien-1-ol C₁₅ H₂₆ O CRDAMVZIKSXKFV-FBXUGWQNSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.223
R-Value Work: 0.182
R-Value Observed: 0.186
Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.9	α = 90
b = 105.9	β = 90
c = 54.38	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-10-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22277051, 22193071, 22107048, 22077062, 81991522, 81991524
Other government	China	BK20220123

Revision History (Full details and data files)

Version 1.0: 2023-10-04
Type: Initial release

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 R01GM133198.