2BY3 | pdb_00002by3

Is radiation damage dependent on the dose-rate used during macromolecular crystallography data collection

PDB DOI: https://doi.org/10.2210/pdb2BY3/pdb

Classification: HYDROLASE
Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2005-07-28 Released: 2006-02-06
Deposition Author(s): Leiros, H.-K.S., Timmins, J., Ravelli, R.B.G., McSweeney, S.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.204 (Depositor), 0.188 (DCC)
R-Value Work:
0.167 (Depositor)
R-Value Observed:
0.168 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Is Radiation Damage Dependent on the Dose-Rate Used During Macromolecular Crystallography Data Collection?

Leiros, H.-K.S., Timmins, J., Ravelli, R.B.G., Mcsweeney, S.M.

(2006) Acta Crystallogr D Biol Crystallogr 62: 125

PubMed: 16421442 Search on PubMed
DOI: https://doi.org/10.1107/S0907444905033627
Primary Citation Related Structures:
2BXY, 2BXZ, 2BY0, 2BY1, 2BY2, 2BY3, 2BY5, 2BY6, 2BY7, 2BY8, 2BY9, 2BYA

PubMed Abstract:
This paper focuses on the radiation-damage effects when applying the same total X-ray dose to protein crystals at different dose rates. These experiments have been performed on both a selenomethionated protein and on bovine trypsin using dose rates that span nearly two orders of magnitude. The results show no clear dose-rate effect on the global indicators of radiation damage, but a small measurable dose-rate effect could be found when studying specific radiation damage. It is hypothesized that this observed dose-rate effect relates to differences in the steady-state free-radical concentration.

Organizational Affiliation

Macromolecular Crystallography Group, European Synchrotron Radiation Facility (ESRF), 6 Rue Jules Horowitz, 38043 Grenoble, France.

Macromolecule Content

Total Structure Weight: 68.55 kDa
Atom Count: 5,922
Modeled Residue Count: 580
Deposited Residue Count: 602
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MALTOOLIGOSYLTREHALOSE TREHALOHYDROLASE	A	602	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 0 EC: 3.2.1.1 (PDB Primary Data), 3.2.1.141 (UniProt)
UniProt
Find proteins for Q9RX51 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RX51 Go to UniProtKB: Q9RX51
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9RX51
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose	B	2		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G92130SN GlyCosmos: G92130SN

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLC Query on GLC Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
TRS Query on TRS 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]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
BME Query on BME Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900006 Query on PRD_900006	B	trehalose	Oligosaccharide / Nutrient		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.204 (Depositor), 0.188 (DCC)
R-Value Work: 0.167 (Depositor)
R-Value Observed: 0.168 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.505	α = 90
b = 66.645	β = 90
c = 152.996	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-02-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-02-06
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
Version 2.1: 2025-04-09
Changes: Advisory, Data collection, Database references, Structure summary