8B4M | pdb_00008b4m

Crystal structure of a hydropyrene synthase (M75L variant) in its closed conformation

PDB DOI: https://doi.org/10.2210/pdb8B4M/pdb

Classification: LYASE
Organism(s): Streptomyces clavuligerus
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2022-09-20 Released: 2023-10-04
Deposition Author(s): Helmer, C.P.O., Driller, R., Loll, B.
Funding Organization(s): German-Israeli Foundation for Research and Development

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.04 Å
R-Value Free:
0.307 (Depositor), 0.308 (DCC)
R-Value Work:
0.252 (Depositor), 0.254 (DCC)
R-Value Observed:
0.255 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 8B4M

Ligand Structure Quality Assessment

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

Literature

A methionine-lined active site governs carbocation stabilization and product specificity in a bacterial terpene synthase

Ringel, M., Helmer, C.P.O., Zev, S., Driller, R., Buhr, E., Reinbold, M., Schwartz, R., Foley, G., Boden, M., Garbe, D., Schenk, G., Major, D.T., Loll, B., Bruck, T.

(2026) FEBS Lett

DOI: https://doi.org/10.1002/1873-3468.70325

Macromolecule Content

Total Structure Weight: 217.12 kDa
Atom Count: 14,633
Modeled Residue Count: 1,841
Deposited Residue Count: 1,932
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Terpene synthase	A, B, C, D, E A, B, C, D, E, F	322	Streptomyces clavuligerus	Mutation(s): 1 Gene Names: SCLAV_p0765 EC: 4.2.3 (PDB Primary Data), 4.2.3.203 (UniProt), 4.2.3.202 (UniProt), 4.2.3.201 (UniProt)
UniProt
Find proteins for D5SK09 (Streptomyces clavuligerus) Explore D5SK09 Go to UniProtKB: D5SK09
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D5SK09
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
212 Query on 212 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain N [auth D] SDF format, chain R [auth E] SDF format, chain V [auth F] MOL2 format, chain J [auth B] MOL2 format, chain N [auth D] MOL2 format, chain R [auth E] MOL2 format, chain V [auth F] mmCIF format, chain J [auth B] mmCIF format, chain N [auth D] mmCIF format, chain R [auth E] mmCIF format, chain V [auth F]	J [auth B], N [auth D], R [auth E], V [auth F]	ALENDRONATE C₄ H₁₃ N O₇ P₂ OGSPWJRAVKPPFI-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain N [auth D] Focus chain R [auth E] Focus chain V [auth F] Interactions & Density Focus chain J [auth B] Focus chain N [auth D] Focus chain R [auth E] Focus chain V [auth F]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain K [auth D] SDF format, chain O [auth E] SDF format, chain P [auth E] SDF format, chain S [auth F] SDF format, chain U [auth F] SDF format, chain T [auth F] SDF format, chain Q [auth E] SDF format, chain M [auth D] SDF format, chain L [auth D] SDF format, chain I [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain K [auth D] MOL2 format, chain O [auth E] MOL2 format, chain P [auth E] MOL2 format, chain S [auth F] MOL2 format, chain U [auth F] MOL2 format, chain T [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain M [auth D] MOL2 format, chain L [auth D] MOL2 format, chain I [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain K [auth D] mmCIF format, chain O [auth E] mmCIF format, chain P [auth E] mmCIF format, chain S [auth F] mmCIF format, chain U [auth F] mmCIF format, chain T [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain M [auth D] mmCIF format, chain L [auth D] mmCIF format, chain I [auth B]	G [auth B] H [auth B] I [auth B] K [auth D] L [auth D] G [auth B], H [auth B], I [auth B], K [auth D], L [auth D], M [auth D], O [auth E], P [auth E], Q [auth E], S [auth F], T [auth F], U [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth E] Focus chain S [auth F] Focus chain T [auth F] Focus chain U [auth F] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth E] Focus chain S [auth F] Focus chain T [auth F] Focus chain U [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.04 Å
R-Value Free: 0.307 (Depositor), 0.308 (DCC)
R-Value Work: 0.252 (Depositor), 0.254 (DCC)
R-Value Observed: 0.255 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.722	α = 90
b = 82.316	β = 92.31
c = 148.294	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
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: 2023-10-04

Deposition Author(s):

Funding Organization	Location	Grant Number
German-Israeli Foundation for Research and Development	Germany	I-85-302.14-2018

Revision History (Full details and data files)

Version 1.0: 2023-10-04
Type: Initial release
Version 1.1: 2026-03-25
Changes: Database references, 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.