7VMW | pdb_00007vmw

Crystal structure of LimF prenyltransferase bound with a peptide substrate and GSPP

PDB DOI: https://doi.org/10.2210/pdb7VMW/pdb

Classification: TRANSFERASE
Organism(s): Limnothrix sp. CACIAM 69d, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-10-09 Released: 2022-08-03
Deposition Author(s): Hamada, K., Kobayashi, S., Okada, C., Zhang, Y., Inoue, S., Goto, Y., Suga, H., Ogata, K., Sengoku, T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free:
0.232 (Depositor), 0.230 (DCC)
R-Value Work:
0.182 (Depositor), 0.181 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

LimF is a versatile prenyltransferase for histidine-C-geranylation on diverse non-natural substrates

Zhang, Y., Hamada, K., Nguyen, D.T., Inoue, S., Satake, M., Kobayashi, S., Okada, C., Ogata, K., Okada, M., Sengoku, T., Goto, Y., Suga, H.

(2022) Nat Catal

DOI: https://doi.org/10.1038/s41929-022-00822-2

Macromolecule Content

Total Structure Weight: 70.53 kDa
Atom Count: 5,305
Modeled Residue Count: 597
Deposited Residue Count: 611
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LynF/TruF/PatF family peptide O-prenyltransferase	A, B	302	Limnothrix sp. CACIAM 69d	Mutation(s): 0 Gene Names: BJG00_018450
UniProt
Find proteins for A0ACD6BAH7 (Limnothrix sp. CACIAM 69d) Explore A0ACD6BAH7 Go to UniProtKB: A0ACD6BAH7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6BAH7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
substrate peptide	C	7	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GST (Subject of Investigation/LOI) Query on GST Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	GERANYL S-THIOLODIPHOSPHATE C₁₀ H₂₀ O₆ P₂ S AKIXWSDUEPPMKM-JXMROGBWSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
PPV (Subject of Investigation/LOI) Query on PPV Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	PYROPHOSPHATE H₄ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.232 (Depositor), 0.230 (DCC)
R-Value Work: 0.182 (Depositor), 0.181 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.66	α = 90
b = 48.43	β = 117.869
c = 91.04	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-08-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-08-03
Type: Initial release
Version 1.1: 2022-08-10
Changes: Structure summary
Version 1.2: 2022-08-24
Changes: Database references
Version 1.3: 2023-11-29
Changes: Data collection, Refinement description
Version 1.4: 2024-10-09
Changes: Structure summary

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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.