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- PDB-1soi: CRYSTAL STRUCTURE OF NUDIX HYDROLASE DR1025 IN COMPLEX WITH SM+3 -

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Basic information

Entry
Database: PDB / ID: 1soi
TitleCRYSTAL STRUCTURE OF NUDIX HYDROLASE DR1025 IN COMPLEX WITH SM+3
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
SAMARIUM (III) ION / Nudix hydrolase DR_1025
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 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 15, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MutT/nudix family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0414
Polymers17,5901
Non-polymers4513
Water1,856103
1
A: MutT/nudix family protein
hetero molecules

A: MutT/nudix family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0828
Polymers35,1802
Non-polymers9026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)53.171, 53.171, 121.972
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsAsymmetric unit of the crystal structure is a monomer whereas biological unit is a dimer. The second part of the biological assembly is generated by using the operator : -X,-Y,Z+1/2

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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): BL21 Tuner cells / References: UniProt: Q9RVK2
#2: Chemical ChemComp-SM / SAMARIUM (III) ION


Mass: 150.360 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Sm
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: sodium acetate, sodium formate, pH 4.50, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1.2 / Wavelength: 1.2 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 2002
RadiationMonochromator: SINGLE CRYSTAL SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. all: 16944 / Num. obs: 16652 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 43.2
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 43.2 / Num. unique all: 16944 / % possible all: 50

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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: 1.8→26.6 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 187.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1671 9.9 %RANDOM
Rwork0.218 ---
all0.221 16652 --
obs0.218 16652 99.2 %-
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 error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.075 Å0.026 Å
Refinement stepCycle: LAST / Resolution: 1.8→26.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1229 0 3 103 1335
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.266
X-RAY DIFFRACTIONc_dihedral_angle_d23.51
X-RAY DIFFRACTIONc_improper_angle_d0.748
LS refinement shellResolution: 1.8→1.86 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.26 143 10 %
Rwork0.228 3 -
obs-1463 89.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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