7FHB | pdb_00007fhb

Structure of prenyltransferase from Streptomyces sp. (strain CL190) with bound GPP

PDB DOI: https://doi.org/10.2210/pdb7FHB/pdb

Classification: TRANSFERASE
Organism(s): Streptomyces sp. CL190
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-07-29 Released: 2022-06-22
Deposition Author(s): Xue, B., Lim, K.J.H., Hartono, Y.D., Go, M.D.K., Fan, H., Yew, W.S.
Funding Organization(s): National Research Foundation (NRF, Singapore)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.222 (Depositor), 0.210 (DCC)
R-Value Work:
0.176 (Depositor), 0.180 (DCC)
R-Value Observed:
0.179 (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

Structure-Guided Engineering of Prenyltransferase NphB for High-Yield and Regioselective Cannabinoid Production.

Lim, K.J.H., Hartono, Y.D., Xue, B., Go, M.K., Fan, H., Yew, W.S.

(2022) ACS Catal 12: 4628-4639

DOI: https://doi.org/10.1021/acscatal.2c00786

Macromolecule Content

Total Structure Weight: 34.25 kDa
Atom Count: 2,669
Modelled Residue Count: 306
Deposited Residue Count: 309
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prenyltransferase	A	309	Streptomyces sp. CL190	Mutation(s): 0
UniProt
Find proteins for Q4R2T2 (Streptomyces sp. (strain CL190)) Explore Q4R2T2 Go to UniProtKB: Q4R2T2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4R2T2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GPP (Subject of Investigation/LOI) Query on GPP 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]	GERANYL DIPHOSPHATE C₁₀ H₂₀ O₇ P₂ GVVPGTZRZFNKDS-JXMROGBWSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.222 (Depositor), 0.210 (DCC)
R-Value Work: 0.176 (Depositor), 0.180 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.462	α = 90
b = 78.36	β = 90
c = 84.992	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-06-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Singapore)	Singapore	--

Revision History (Full details and data files)

Version 1.0: 2022-06-22
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, 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.