1UMP | pdb_00001ump

GEOMETRY OF TRITERPENE CONVERSION TO PENTACARBOCYCLIC HOPENE

PDB DOI: https://doi.org/10.2210/pdb1UMP/pdb

Classification: ISOMERASE
Organism(s): Alicyclobacillus acidocaldarius
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2003-08-27 Released: 2004-02-03
Deposition Author(s): Reinert, D.J., Balliano, G., Schulz, G.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free:
0.228 (Depositor), 0.236 (DCC)
R-Value Work:
0.186 (Depositor), 0.196 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Conversion of Squalene to the Pentacarbocyclic Hopene

Reinert, D.J., Balliano, G., Schulz, G.E.

(2004) Chem Biol 11: 121

PubMed: 15113001 Search on PubMed
DOI: https://doi.org/10.1016/j.chembiol.2003.12.013
Primary Citation Related Structures:
1UMP

PubMed Abstract:
The membrane protein squalene-hopene cyclase was cocrystallized with 2-azasqualene and analyzed by X-ray diffraction to 2.13 A resolution. The conformation of this close analog was clearly established, and it agreed with the common textbook presentation. The bound squalene undergoes only small conformational changes during the formation of rings A through D, thus requiring no intermediate. However, ring E formation is hindered by an entropic barrier, which may explain its absence in the steroids. The structure analysis revealed a mobile region between the active center cavity and the membrane, which may melt, opening a passage for squalene and hopene.

Organizational Affiliation

Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstr. 21, D-79104 Freiburg, Germany.

Macromolecule Content

Total Structure Weight: 217.72 kDa
Atom Count: 16,339
Modeled Residue Count: 1,860
Deposited Residue Count: 1,893
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SQUALENE--HOPENE CYCLASE	A, B, C	631	Alicyclobacillus acidocaldarius	Mutation(s): 0 EC: 5.4.99.17 (PDB Primary Data), 4.2.1.129 (UniProt)
UniProt
Find proteins for P33247 (Alicyclobacillus acidocaldarius subsp. acidocaldarius (strain ATCC 27009 / DSM 446 / BCRC 14685 / JCM 5260 / KCTC 1825 / NBRC 15652 / NCIMB 11725 / NRRL B-14509 / 104-IA)) Explore P33247 Go to UniProtKB: P33247
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33247
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SQA Query on SQA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C]	E [auth A], H [auth B], K [auth C]	2-AZASQUALENE C₂₉ H₅₁ N OBYAAZRQFIVRJS-GUUMBNHASA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C]
C8E Query on C8E Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain J [auth C] SDF format, chain I [auth C] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] MOL2 format, chain I [auth C] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C] mmCIF format, chain I [auth C]	D [auth A], F [auth B], G [auth B], I [auth C], J [auth C]	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE C₁₆ H₃₄ O₅ FEOZZFHAVXYAMB-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth C] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free: 0.228 (Depositor), 0.236 (DCC)
R-Value Work: 0.186 (Depositor), 0.196 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.144	α = 90
b = 139.144	β = 90
c = 240.699	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2004-02-03

Deposition Author(s):

Reinert, D.J.

Balliano, G.

Schulz, G.E.

Revision History (Full details and data files)

Version 1.0: 2004-02-03
Type: Initial release
Version 1.1: 2013-11-20
Changes: Derived calculations, Non-polymer description, Other, Source and taxonomy, Version format compliance
Version 1.2: 2019-05-08
Changes: Data collection, Experimental preparation, Other
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description