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- PDB-1sjy: Crystal Structure of NUDIX HYDROLASE DR1025 FROM DEINOCOCCUS RADI... -

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Basic information

Entry
Database: PDB / ID: 1sjy
TitleCrystal Structure of NUDIX HYDROLASE DR1025 FROM DEINOCOCCUS RADIODURANS
ComponentsMutT/nudix family protein
KeywordsHYDROLASE / NUDIX FOLD / alpha-beta-alpha sandwich / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


8-oxo-(d)GTP phosphatase / diadenosine hexaphosphate hydrolase (ATP-forming) / hydrolase activity / ATP binding / metal ion binding
Similarity search - Function
: / NUDIX hydrolase / 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 ...: / NUDIX hydrolase / 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_1025
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.39 Å
AuthorsRanatunga, W. / Hill, E.E. / Mooster, J.L. / Holbrook, E.L. / Schulze-Gahmen, U. / Xu, W. / Bessman, M.J. / Brenner, S.E. / Holbrook, S.R. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Structural Studies of the Nudix Hydrolase DR1025 From Deinococcus radiodurans and its Ligand Complexes.
Authors: Ranatunga, W. / Hill, E.E. / Mooster, J.L. / Holbrook, E.L. / Schulze-Gahmen, U. / Xu, W. / Bessman, M.J. / Brenner, S.E. / Holbrook, S.R.
History
DepositionMar 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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: MutT/nudix family protein


Theoretical massNumber of molelcules
Total (without water)17,5901
Polymers17,5901
Non-polymers00
Water1,838102
1
A: MutT/nudix family protein

A: MutT/nudix family protein


Theoretical massNumber of molelcules
Total (without water)35,1802
Polymers35,1802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)53.210, 53.210, 122.516
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe asymmetric unit of a crystal structure contains one biological unit

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Components

#1: Protein MutT/nudix family protein


Mass: 17589.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: DR1025 / Plasmid: PET24A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Tuner
References: UniProt: Q9RVK2, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.45 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: sodium acetate, sodium formate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Temp details: K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 2002
RadiationMonochromator: Si(220), cylindrically bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.39→100 Å / Num. all: 35337 / Num. obs: 35334 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.6 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 56.1
Reflection shellResolution: 1.39→1.44 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 4.4 / Num. unique all: 35874 / Rsym value: 0.058 / % possible all: 89.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
CNS1.1phasing
RefinementMethod to determine structure: SAD / Resolution: 1.39→100 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1092.6 / Data cutoff low absF: 4.3 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.242 3520 9.9 %RANDOM
Rwork0.228 ---
all0.229 35537 --
obs0.228 35334 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.8 Å2 / ksol: 0.47 e/Å3
Displacement parametersBiso mean: 17.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.822 Å20 Å20 Å2
2---0.822 Å20 Å2
3---1.645 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.06 Å0.03 Å
Refinement stepCycle: LAST / Resolution: 1.39→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1219 0 0 102 1321
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.278
X-RAY DIFFRACTIONc_dihedral_angle_d23.47
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.115
X-RAY DIFFRACTIONc_mcangle_it1.79
X-RAY DIFFRACTIONc_scbond_it1.846
X-RAY DIFFRACTIONc_scangle_it2.654
LS refinement shellResolution: 1.39→1.44 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.326 386 10 %
Rwork0.281 3 -
obs-35874 89.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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