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), 0.211 (DCC)
R-Value Work:
0.176 (Depositor), 0.176 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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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
Modeled Residue Count: 306
Deposited Residue Count: 309
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.211 (DCC)
R-Value Work: 0.176 (Depositor), 0.176 (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

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Ligand Structure Quality Assessment

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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

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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.