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- PDB-2o5f: Crystal Structure of DR0079 from Deinococcus radiodurans at 1.9 A... -

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Basic information

Entry
Database: PDB / ID: 2o5f
TitleCrystal Structure of DR0079 from Deinococcus radiodurans at 1.9 Angstrom Resolution
ComponentsPutative Nudix hydrolase DR_0079
KeywordsHYDROLASE / alpha plus beta / nudix hydrolase
Function / homology
Function and homology information


nucleotide metabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / hydrolase activity / nucleotide binding / magnesium ion binding
Similarity search - Function
NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Nudix hydrolase DR_0079
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsKennedy, M.A. / Buchko, G.W. / Ni, S. / Robinson, H.
CitationJournal: Biochemistry / Year: 2008
Title: Functional and Structural Characterization of DR_0079 from Deinococcus radiodurans, a Novel Nudix Hydrolase with a Preference for Cytosine (Deoxy)ribonucleoside 5'-Di- and Triphosphates.
Authors: Buchko, G.W. / Litvinova, O. / Robinson, H. / Yakunin, A.F. / Kennedy, M.A.
History
DepositionDec 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative Nudix hydrolase DR_0079
B: Putative Nudix hydrolase DR_0079


Theoretical massNumber of molelcules
Total (without water)38,6072
Polymers38,6072
Non-polymers00
Water3,081171
1
A: Putative Nudix hydrolase DR_0079


Theoretical massNumber of molelcules
Total (without water)19,3041
Polymers19,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative Nudix hydrolase DR_0079


Theoretical massNumber of molelcules
Total (without water)19,3041
Polymers19,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.019, 156.554, 126.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Putative Nudix hydrolase DR_0079


Mass: 19303.561 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: R1 / Gene: DR0079 / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): K12 BL21 (DE3)
References: UniProt: Q9RY71, Hydrolases; Acting on acid anhydrides
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 1) 30% PEG 4000, 0.1M sodium citrate, pH 5.6, 0.2M ammonium acetate, or 2) 30% PEG 4000, 0.1 M Tris-HCl, pH 8.5, 0.2 M lithium sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A11.1
SYNCHROTRONNSLS X29A20.9792
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 22, 2005
Details: Rosenbaum-Rock double crystal dagital focusing monochromator and vertical focusing mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si-111SINGLE WAVELENGTHMx-ray1
2Si-111SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.97921
ReflectionResolution: 1.9→50 Å / Num. all: 27131 / Num. obs: 27095 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rsym value: 0.071 / Net I/σ(I): 49.57
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 8.45 / Rsym value: 0.268 / % possible all: 97.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Highest resolution: 1.9 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2674 1347 -random
Rwork0.2335 ---
all-27095 --
obs-26844 99.4 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.797 Å2--
2--4.025 Å2-
3---6.772 Å2
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2535 0 0 171 2706
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.0056
X-RAY DIFFRACTIONx_dihedral_angle_d1.2411
LS refinement shellHighest resolution: 1.9 Å
RfactorNum. reflection% reflection
Rfree0.2674 1347 -
Rwork0.2335 --
obs-26844 99.4 %

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