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- PDB-2jao: Crystal structure of D12N variant of mouse cytosolic 5'(3')- deox... -

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Basic information

Entry
Database: PDB / ID: 2jao
TitleCrystal structure of D12N variant of mouse cytosolic 5'(3')- deoxyribonucleotidase (cdN) in complex with deoxyguanosine 5'- monophosphate
Components5'(3')-DEOXYRIBONUCLEOTIDASE
KeywordsHYDROLASE / NUCLEOTIDE METABOLISM / NUCLEOTIDE-BINDING / ALPHA-BETA FOLD / METAL-BINDING / MAGNESIUM / CYTOSOL
Function / homology
Function and homology information


Purine catabolism / pyrimidine nucleotide binding / Pyrimidine catabolism / dTMP catabolic process / dCMP catabolic process / dGMP catabolic process / UMP catabolic process / amide catabolic process / dUMP catabolic process / : ...Purine catabolism / pyrimidine nucleotide binding / Pyrimidine catabolism / dTMP catabolic process / dCMP catabolic process / dGMP catabolic process / UMP catabolic process / amide catabolic process / dUMP catabolic process / : / IMP catabolic process / deoxyribonucleotide catabolic process / allantoin metabolic process / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / 5'-nucleotidase activity / phosphatase activity / mitochondrion / metal ion binding / identical protein binding / nucleus / cytosol
Similarity search - Function
5'(3')-deoxyribonucleotidase / 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C) / Deoxyribonucleotidase; domain 2 / Ribonucleotide Reductase Protein R1; domain 1 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...5'(3')-deoxyribonucleotidase / 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C) / Deoxyribonucleotidase; domain 2 / Ribonucleotide Reductase Protein R1; domain 1 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / 5'(3')-deoxyribonucleotidase, cytosolic type
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWallden, K. / Ruzzenente, B. / Bianchi, V. / Nordlund, P.
CitationJournal: Biochemistry / Year: 2007
Title: Crystal Structures of Human and Murine Deoxyribonucleotidases: Insights Into Recognition of Substrates and Nucleotide Analogues.
Authors: Wallden, K. / Rinaldo-Matthis, A. / Ruzzenente, B. / Rampazzo, C. / Bianchi, V. / Nordlund, P.
History
DepositionNov 29, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 15, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: chem_comp / exptl_crystal_grow ...chem_comp / exptl_crystal_grow / pdbx_struct_special_symmetry / struct_biol
Item: _chem_comp.type / _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.5May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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.pdbx_ptnr1_label_alt_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_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

Downloads & links

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Assembly

Deposited unit
A: 5'(3')-DEOXYRIBONUCLEOTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5694
Polymers23,1051
Non-polymers4643
Water3,153175
1
A: 5'(3')-DEOXYRIBONUCLEOTIDASE
hetero molecules

A: 5'(3')-DEOXYRIBONUCLEOTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1388
Polymers46,2112
Non-polymers9276
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
Buried area4690 Å2
ΔGint-48.4 kcal/mol
Surface area18270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.250, 76.250, 85.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-2036-

HOH

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Components

#1: Protein 5'(3')-DEOXYRIBONUCLEOTIDASE / CYTOSOLIC TYPE / CYTOSOLIC 5' / 3'-PYRIMIDINE NUCLEOTIDASE / DEOXY-5'-NUCLEOTIDASE 1 / DNT-1 / ...CYTOSOLIC TYPE / CYTOSOLIC 5' / 3'-PYRIMIDINE NUCLEOTIDASE / DEOXY-5'-NUCLEOTIDASE 1 / DNT-1 / CYTOSOLIC DEOXYRIBONUCLEOTIDASE


Mass: 23105.482 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS
References: UniProt: Q9JM14, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-DGP / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 12 TO ASN

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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: 3.2 Å3/Da / Density % sol: 61.1 % / Description: NONE
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M MAGNESIUM CHLORIDE, 0.1 M BIS-TRIS PH 5.5, 23-25% PEG3350 AT 6 DEGREES CELSIUS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.141
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.141 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 19090 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.84
Reflection shellResolution: 2→2.1 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 5.91 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0032refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→66.08 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.224 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.205 985 5.1 %RANDOM
Rwork0.165 ---
obs0.167 18178 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.74 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→66.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1595 0 30 175 1800
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221717
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.561.9962344
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.975210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90923.48389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63515297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4151518
X-RAY DIFFRACTIONr_chiral_restr0.1150.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021327
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.2623
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21114
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2130
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0420.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1291.51055
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.66721638
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4143786
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8184.5698
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 64 -
Rwork0.194 1352 -
obs--100 %

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