3ZXS | pdb_00003zxs

Cryptochrome B from Rhodobacter sphaeroides

PDB DOI: https://doi.org/10.2210/pdb3ZXS/pdb

Classification: LYASE
Organism(s): Cereibacter sphaeroides 2.4.1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-08-15 Released: 2012-02-15
Deposition Author(s): Geisselbrecht, Y., Fruhwirth, S., Pierik, A.J., Klug, G., Essen, L.-O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.228 (Depositor), 0.220 (DCC)
R-Value Work:
0.198 (Depositor), 0.200 (DCC)
R-Value Observed:
0.199 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Cryb from Rhodobacter Sphaeroides: A Unique Class of Cryptochromes with New Cofactors.

Geisselbrecht, Y., Fruhwirth, S., Schroeder, C., Pierik, A.J., Klug, G., Essen, L.-O.

(2012) EMBO Rep 13: 223

PubMed: 22290493 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/embor.2012.2
Primary Citation of Related Structures:
3ZXS

PubMed Abstract:
Cryptochromes and photolyases are structurally related but have different biological functions in signalling and DNA repair. Proteobacteria and cyanobacteria harbour a new class of cryptochromes, called CryPro. We have solved the 2.7 Å structure of one of its members, cryptochrome B from Rhodobacter sphaeroides, which is a regulator of photosynthesis gene expression. The structure reveals that, in addition to the photolyase-like fold, CryB contains two cofactors only conserved in the CryPro subfamily: 6,7-dimethyl-8-ribityl-lumazine in the antenna-binding domain and a [4Fe-4S] cluster within the catalytic domain. The latter closely resembles the iron-sulphur cluster harbouring the large primase subunit PriL, indicating that PriL is evolutionarily related to the CryPro class of cryptochromes.

Organizational Affiliation

Department of Chemistry-Institute of Biochemistry, Philipps-University, Marburg, Germany.

Macromolecule Content

Total Structure Weight: 184.42 kDa
Atom Count: 12,654
Modelled Residue Count: 1,521
Deposited Residue Count: 1,566
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRYPTOCHROME B	A, B, C	522	Cereibacter sphaeroides 2.4.1	Mutation(s): 0
UniProt
Find proteins for Q3IXP1 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3IXP1 Go to UniProtKB: Q3IXP1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3IXP1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] SDF format, chain N [auth C] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain N [auth C] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain N [auth C]	D [auth A], I [auth B], N [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Focus chain N [auth C] Interactions & Density Focus chain D [auth A] Focus chain I [auth B] Focus chain N [auth C]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain E [auth A] SDF format, chain O [auth C] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain O [auth C] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain O [auth C]	E [auth A], J [auth B], O [auth C]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C]
DLZ Query on DLZ Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain P [auth C] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain P [auth C] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain P [auth C] mmCIF format, chain K [auth B]	F [auth A], K [auth B], P [auth C]	1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol C₁₃ H₁₈ N₄ O₆ SXDXRJZUAJBNFL-XKSSXDPKSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain P [auth C] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain P [auth C]
GD Query on GD Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain R [auth C] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C]	H [auth A], M [auth B], R [auth C]	GADOLINIUM ATOM Gd UIWYJDYFSGRHKR-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain R [auth C] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain R [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain Q [auth C] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth C]	G [auth A], L [auth B], Q [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain Q [auth C] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain Q [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.228 (Depositor), 0.220 (DCC)
R-Value Work: 0.198 (Depositor), 0.200 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.84	α = 90
b = 137.84	β = 90
c = 521.94	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-02-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-02-15
Type: Initial release
Version 1.1: 2012-03-28
Changes: Other
Version 1.2: 2014-08-13
Changes: Refinement description
Version 1.3: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

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Cryptochrome B from Rhodobacter sphaeroides

Cryb from Rhodobacter Sphaeroides: A Unique Class of Cryptochromes with New Cofactors.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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