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), 0.280 (DCC)
R-Value Work:
0.237 (Depositor), 0.240 (DCC)
R-Value Observed:
0.239 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

crystal structure of s hydropyrene synthase in its closed conformation

Helmer, C.P.O., Driller, R., Loll, B.

To be published.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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