2BIW | pdb_00002biw

Crystal structure of apocarotenoid cleavage oxygenase from Synechocystis, native enzyme

PDB DOI: https://doi.org/10.2210/pdb2BIW/pdb

Classification: OXIDOREDUCTASE
Organism(s): Synechocystis sp. PCC 6803
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2005-01-26 Released: 2005-04-14
Deposition Author(s): Kloer, D.P., Ruch, S., Al-Babili, S., Beyer, P., Schulz, G.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.224 (Depositor), 0.229 (DCC)
R-Value Work:
0.180 (Depositor), 0.187 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: other
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Ligand Structure Quality Assessment

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Literature

The Structure of a Retinal-Forming Carotenoid Oxygenase

Kloer, D.P., Ruch, S., Al-Babili, S., Beyer, P., Schulz, G.E.

(2005) Science 308: 267

PubMed: 15821095 Search on PubMed
DOI: https://doi.org/10.1126/science.1108965
Primary Citation Related Structures:
2BIW, 2BIX

PubMed Abstract:
Enzymes that produce retinal and related apocarotenoids constitute a sequence- and thus structure-related family, a member of which was analyzed by x-ray diffraction. This member is an oxygenase and contains an Fe2+-4-His arrangement at the axis of a seven-bladed beta-propeller chain fold covered by a dome formed by six large loops. The Fe2+ is accessible through a long nonpolar tunnel that holds a carotenoid derivative in one of the crystals. On binding, three consecutive double bonds of this carotenoid changed from a straight all-trans to a cranked cis-trans-cis conformation. The remaining trans bond is located at the dioxygen-ligated Fe2+ and cleaved by oxygen.

Organizational Affiliation

Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany.

Macromolecule Content

Total Structure Weight: 219.34 kDa
Atom Count: 15,742
Modeled Residue Count: 1,916
Deposited Residue Count: 1,960
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
APOCAROTENOID-CLEAVING OXYGENASE	A, B, C, D	490	Synechocystis sp. PCC 6803	Mutation(s): 0 EC: 1.13.11.75
UniProt
Find proteins for P74334 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P74334 Go to UniProtKB: P74334
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P74334
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3ON Query on 3ON Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain K [auth D] SDF format, chain I [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C]	E [auth A], G [auth B], I [auth C], K [auth D]	(3R)-3-HYDROXY-8'-APOCAROTENOL C₃₀ H₄₂ O₂ FNAJVVMDXCOSFY-VFGOXHQXSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.224 (Depositor), 0.229 (DCC)
R-Value Work: 0.180 (Depositor), 0.187 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.046	α = 90
b = 125.278	β = 90
c = 203.086	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2005-04-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-04-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2024-05-01
Changes: Data collection, Database references, Derived calculations, Other, Refinement description