2J07 | pdb_00002j07

Thermus DNA photolyase with 8-HDF antenna chromophore

PDB DOI: https://doi.org/10.2210/pdb2J07/pdb

Classification: LYASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2006-08-01 Released: 2007-05-01
Deposition Author(s): Klar, T., Kaiser, G., Hennecke, U., Carell, T., Batschauer, A., Essen, L.-O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.212 (Depositor), 0.220 (DCC)
R-Value Work:
0.169 (Depositor), 0.170 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Natural and Non-Natural Antenna Chromophores in the DNA Photolyase from Thermus Thermophilus

Klar, T., Kaiser, G., Hennecke, U., Carell, T., Batschauer, A., Essen, L.-O.

(2006) Chembiochem 7: 1798

PubMed: 17051659 Search on PubMed
DOI: https://doi.org/10.1002/cbic.200600206
Primary Citation of Related Structures:
2J07, 2J08, 2J09

PubMed Abstract:
X-ray crystallographic and functional analysis of the class I DNA photolyase from Thermus thermophilus revealed the binding of flavin mononucleotide (FMN) as an antenna chromophore. The binding mode of FMN closely coincides with the binding of a deazaflavin-like chromophore in the related class I DNA photolyase from Anacystis nidulans. Compared to the R46E mutant, which lacks a conserved arginine in the binding site for the antenna chromophore, the FMN-comprising holophotolyase exhibits an eightfold higher activity at 450 nm. The facile incorporation of the flavin cofactors 8-hydroxy-deazariboflavin and 8-iodo-8-demethyl-riboflavin into the binding site for the antenna chromophore paves the way for wavelength-tuning of the activity spectra of DNA photolyases by using synthetic flavins.

Organizational Affiliation

Philipps-Universität Marburg, Fachbereich Chemie, Hans-Meerwein-Strasse, 35032 Marburg, Germany.

Macromolecule Content

Total Structure Weight: 49.32 kDa
Atom Count: 3,836
Modelled Residue Count: 419
Deposited Residue Count: 420
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DEOXYRIBODIPYRIMIDINE PHOTO-LYASE	A	420	Thermus thermophilus HB8	Mutation(s): 0 EC: 4.1.99.3
UniProt
Find proteins for P61497 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P61497 Go to UniProtKB: P61497
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61497
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
HDF Query on HDF Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	8-HYDROXY-10-(D-RIBO-2,3,4,5-TETRAHYDROXYPENTYL)-5-DEAZAISOALLOXAZINE C₁₆ H₁₇ N₃ O₇ AUEILLWDYUBWCM-AGIUHOORSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	D [auth A], E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.212 (Depositor), 0.220 (DCC)
R-Value Work: 0.169 (Depositor), 0.170 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.62	α = 90
b = 112.62	β = 90
c = 140.262	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-05-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-05-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-07-05
Changes: Data collection
Version 1.3: 2023-12-13
Changes: Advisory, Data collection, Database references, Other, Refinement description