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- PDB-1sz3: CRYSTAL STRUCTURE OF NUDIX HYDROLASE DR1025 IN COMPLEXED WITH GNP... -

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Basic information

Entry
Database: PDB / ID: 1sz3
TitleCRYSTAL STRUCTURE OF NUDIX HYDROLASE DR1025 IN COMPLEXED WITH GNP AND MG+2
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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Nudix hydrolase DR_1025
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
DepositionApr 2, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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.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
B: MutT/nudix family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2736
Polymers35,1802
Non-polymers1,0934
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-36 kcal/mol
Surface area14310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.072, 53.072, 122.197
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
DetailsAsymmetric unit of the crystal structure is a dimer and the biological unit is a dimer.

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Components

#1: Protein MutT/nudix family protein


Mass: 17589.936 Da / Num. of mol.: 2
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
References: UniProt: Q9RVK2, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.44 Å3/Da / Density % sol: 47.75 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 9, 2003
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 44415 / Num. obs: 44122 / % possible obs: 97.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 47.35
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.78 / Num. unique all: 44122 / Rsym value: 0.4735 / % possible all: 86.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data scaling
CNS1.1refinement
HKL-2000data reduction
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→50 Å / Data cutoff high absF: 1734.3 / 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
Rfree0.234 4346 10 %RANDOM
Rwork0.213 ---
all0.215 43122 --
obs0.213 43122 97.1 %-
Solvent computationSolvent model: FLAT MODEL
Displacement parametersBiso mean: 17.75 Å2
Baniso -1Baniso -2Baniso -3
1--1.474 Å20 Å20 Å2
2---1.474 Å20 Å2
3---2.947 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2454 0 66 223 2743
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.762
X-RAY DIFFRACTIONc_dihedral_angle_d24.312
X-RAY DIFFRACTIONc_improper_angle_d4.135
X-RAY DIFFRACTIONc_mcbond_it1.455
X-RAY DIFFRACTIONc_mcangle_it2.359
X-RAY DIFFRACTIONc_scbond_it2.739
X-RAY DIFFRACTIONc_scangle_it3.112
LS refinement shellResolution: 1.6→1.66 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2783 390 9.8 %
Rwork0.2451 3943 -
obs-3553 89 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3GNP.PARAM

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