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- PDB-3t8i: Structural analysis of thermostable S. solfataricus purine-specif... -

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Basic information

Entry
Database: PDB / ID: 3t8i
TitleStructural analysis of thermostable S. solfataricus purine-specific nucleoside hydrolase
ComponentsPurine nucleosidase, (IunH-2)
KeywordsHYDROLASE / Purine nucleoside hydrolase / thermostable protein / Open (alpha / beta) structure / Rossmann fold / NH-fold / nucleoside hydrolase / Nucleotide metabolism / N-glycosidase
Function / homology
Function and homology information


purine nucleosidase / purine nucleosidase activity / purine nucleoside catabolic process / metal ion binding / cytosol
Similarity search - Function
Inosine/uridine-preferring nucleoside hydrolase, conserved site / Inosine-uridine preferring nucleoside hydrolase family signature. / Inosine-uridine Nucleoside N-ribohydrolase; Chain A / Ribonucleoside hydrolase-like / Inosine/uridine-preferring nucleoside hydrolase domain / Inosine-uridine preferring nucleoside hydrolase / Ribonucleoside hydrolase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Purine nucleosidase, putative (IunH-2)
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsMinici, C. / Cacciapuoti, G. / De Leo, E. / Porcelli, M. / Degano, M.
Citation
Journal: Biochemistry / Year: 2012
Title: New Determinants in the Catalytic Mechanism of Nucleoside Hydrolases from the Structures of Two Isozymes from Sulfolobus solfataricus.
Authors: Minici, C. / Cacciapuoti, G. / De Leo, E. / Porcelli, M. / Degano, M.
#1: Journal: Arch.Biochem.Biophys. / Year: 2009
Title: Biochemical characterization and homology modeling of a purine-specific ribonucleoside hydrolase from the archaeon Sulfolobus solfataricus: insights into mechanisms of protein stabilization.
Authors: Porcelli, M. / Peluso, I. / Marabotti, A. / Facchiano, A. / Cacciapuoti, G.
History
DepositionAug 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_asym_id / _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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

Downloads & links

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Assembly

Deposited unit
A: Purine nucleosidase, (IunH-2)
B: Purine nucleosidase, (IunH-2)
C: Purine nucleosidase, (IunH-2)
D: Purine nucleosidase, (IunH-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,19031
Polymers137,0044
Non-polymers2,18627
Water17,312961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13840 Å2
ΔGint-94 kcal/mol
Surface area41190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.760, 81.130, 98.020
Angle α, β, γ (deg.)90.000, 100.700, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22B
13D
23B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETGOLGOL6AA - F1 - 3071
211METMETGOLGOL6BB - M1 - 3071
121SERSERASPASP2AA8 - 138 - 13
221SERSERASPASP2BB8 - 138 - 13
112METMETGOLGOL6CC - V1 - 3071
212METMETGOLGOL6BB - M1 - 3071
113TRPTRPLEULEU2DD200 - 210200 - 210
213TRPTRPLEULEU2BB200 - 210200 - 210

NCS ensembles :
ID
1
2
3
Detailsbiological unit is the same as asym.

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Purine nucleosidase, (IunH-2)


Mass: 34250.988 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: iunH-2, SSO2243 / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97WH6, purine nucleosidase

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Non-polymers , 5 types, 988 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 961 / 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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES, 5% PEG 3350, 5 mM CaCl2, 5 mM CdCl2, 5 mM MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 28, 2009
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. all: 119836 / Num. obs: 119836 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.395 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 14.69
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.90.6192.898682817747198.5
1.9-20.3894.447035514373198.5
2-2.50.1759.3220810242530199.1
2.5-30.07618.479206418899199.4
3-40.04329.477244715074199.6
4-50.0339.64257555425199.7
5-60.03238.931145824121100
6-100.02942.56123082634199.6
10-1000.02446.553212742198

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
DNAdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2MAS

2mas


Resolution: 1.8→96.23 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.794 / SU ML: 0.086 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.121 / Stereochemistry target values: Engh & Huber
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2136 6036 5 %RANDOM
Rwork0.1698 ---
all0.172 119835 --
obs0.172 119835 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 61.55 Å2 / Biso mean: 26.1757 Å2 / Biso min: 5.89 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å20.24 Å2
2--0.6 Å20 Å2
3---1.06 Å2
Refinement stepCycle: LAST / Resolution: 1.8→96.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9660 0 136 961 10757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02210084
X-RAY DIFFRACTIONr_bond_other_d0.0010.026838
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.96313665
X-RAY DIFFRACTIONr_angle_other_deg0.932316812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52251251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69725.262439
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18151785
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3581538
X-RAY DIFFRACTIONr_chiral_restr0.0910.21549
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110993
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021893
X-RAY DIFFRACTIONr_mcbond_it0.7961.56143
X-RAY DIFFRACTIONr_mcbond_other0.2391.52485
X-RAY DIFFRACTIONr_mcangle_it1.35529990
X-RAY DIFFRACTIONr_scbond_it2.15633941
X-RAY DIFFRACTIONr_scangle_it3.2824.53660
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A36TIGHT POSITIONAL0.030.05
1A25MEDIUM POSITIONAL0.060.5
1A3961LOOSE POSITIONAL0.285
1A36TIGHT THERMAL10.5
1A25MEDIUM THERMAL0.962
1A3961LOOSE THERMAL1.2910
2C3993LOOSE POSITIONAL0.325
2C3993LOOSE THERMAL5.3510
3D66TIGHT POSITIONAL0.020.05
3D102MEDIUM POSITIONAL0.040.5
3D66TIGHT THERMAL0.660.5
3D102MEDIUM THERMAL0.392
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 450 -
Rwork0.241 8301 -
all-8751 -
obs--98.19 %

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