8B4L | pdb_00008b4l

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

PDB DOI: https://doi.org/10.2210/pdb8B4L/pdb

Classification: LYASE
Organism(s): Streptomyces clavuligerus
Expression System: Escherichia coli BL21(DE3)
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: 3.39 Å
R-Value Free:
0.275 (Depositor), 0.283 (DCC)
R-Value Work:
0.237 (Depositor), 0.241 (DCC)
R-Value Observed:
0.239 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.3 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: 220.65 kDa
Atom Count: 14,704
Modeled Residue Count: 1,843
Deposited Residue Count: 1,938
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Terpene synthase	A [auth E] B [auth A] C [auth B] D [auth C] E [auth D] A [auth E], B [auth A], C [auth B], D [auth C], E [auth D], F	323	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
AHD Query on AHD Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain V [auth C] SDF format, chain R [auth B] SDF format, chain N [auth A] SDF format, chain J [auth E] SDF format, chain BA [auth F] MOL2 format, chain Z [auth D] MOL2 format, chain V [auth C] MOL2 format, chain R [auth B] MOL2 format, chain N [auth A] MOL2 format, chain J [auth E] MOL2 format, chain BA [auth F] mmCIF format, chain Z [auth D] mmCIF format, chain V [auth C] mmCIF format, chain R [auth B] mmCIF format, chain N [auth A] mmCIF format, chain J [auth E] mmCIF format, chain BA [auth F]	BA [auth F] J [auth E] N [auth A] R [auth B] V [auth C] BA [auth F], J [auth E], N [auth A], R [auth B], V [auth C], Z [auth D]	4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDIPHOSPHONATE C₄ H₉ N O₇ P₂ OGSPWJRAVKPPFI-UHFFFAOYSA-J		Interactions Focus chain BA [auth F] Focus chain J [auth E] Focus chain N [auth A] Focus chain R [auth B] Focus chain V [auth C] Focus chain Z [auth D] Interactions & Density Focus chain BA [auth F] Focus chain J [auth E] Focus chain N [auth A] Focus chain R [auth B] Focus chain V [auth C] Focus chain Z [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain I [auth E] SDF format, chain H [auth E] SDF format, chain G [auth E] SDF format, chain AA [auth F] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain I [auth E] MOL2 format, chain H [auth E] MOL2 format, chain G [auth E] MOL2 format, chain AA [auth F] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain I [auth E] mmCIF format, chain H [auth E] mmCIF format, chain G [auth E] mmCIF format, chain AA [auth F]	AA [auth F] G [auth E] H [auth E] I [auth E] K [auth A] AA [auth F], G [auth E], H [auth E], I [auth E], K [auth A], L [auth A], M [auth A], O [auth B], P [auth B], Q [auth B], S [auth C], T [auth C], U [auth C], W [auth D], X [auth D], Y [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain G [auth E] Focus chain H [auth E] Focus chain I [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain AA [auth F] Focus chain G [auth E] Focus chain H [auth E] Focus chain I [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A [auth E] B [auth A] C [auth B] D [auth C] E [auth D] A [auth E], B [auth A], C [auth B], D [auth C], E [auth D], F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.39 Å
R-Value Free: 0.275 (Depositor), 0.283 (DCC)
R-Value Work: 0.237 (Depositor), 0.241 (DCC)
R-Value Observed: 0.239 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.698	α = 90
b = 176.688	β = 90
c = 185.651	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
SHELXCD	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: 2023-11-15
Changes: Data collection
Version 1.2: 2024-11-20
Changes: Structure summary
Version 1.3: 2026-03-25
Changes: Database references