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

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Basic information

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


Purine catabolism / pyrimidine nucleotide binding / Pyrimidine catabolism / dTMP catabolic process / UMP catabolic process / pyrimidine deoxyribonucleotide catabolic process / dCMP catabolic process / dGMP catabolic process / dUMP catabolic process / amide catabolic process ...Purine catabolism / pyrimidine nucleotide binding / Pyrimidine catabolism / dTMP catabolic process / UMP catabolic process / pyrimidine deoxyribonucleotide catabolic process / dCMP catabolic process / dGMP catabolic process / dUMP catabolic process / amide catabolic process / IMP 5'-nucleotidase activity / IMP catabolic process / deoxyribonucleotide catabolic process / allantoin metabolic process / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / 5'-nucleotidase activity / phosphatase activity / dephosphorylation / mitochondrion / identical protein binding / nucleus / metal ion binding / 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'-DEOXYURIDINE 5'-MONOPHOSPHATE / 5'(3')-deoxyribonucleotidase, cytosolic type
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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 30, 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 1.3May 15, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 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 / struct_conn
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 / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_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

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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)23,4383
Polymers23,1051
Non-polymers3322
Water3,225179
1
A: 5'(3')-DEOXYRIBONUCLEOTIDASE
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)46,8766
Polymers46,2112
Non-polymers6654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
Buried area2810 Å2
ΔGint-23.3 kcal/mol
Surface area21770 Å2
MethodPQS
Unit cell
Length a, b, c (Å)75.309, 75.309, 85.174
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-2033-

HOH

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Components

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


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-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 12 TO ASN
Sequence detailsMAVKRPVRVLVDMDGVLADFESGLLQGFRRRFPEEPHVPLEQRRGFLANEQYGALRPDLA EKVASVYE

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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: ESRF / Beamline: ID14-4 / Wavelength: 0.9395
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 25, 2006 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 1.95→65.23 Å / Num. obs: 20062 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 19
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→40 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.932 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1034 5.1 %RANDOM
Rwork0.156 ---
obs0.158 19307 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: 24.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.03 Å20 Å2
2---0.05 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.94→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1595 0 21 179 1795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221780
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.9892434
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0415220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.99723.62691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84915310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1381518
X-RAY DIFFRACTIONr_chiral_restr0.10.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02404
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1910.2819
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21205
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2168
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2011.51103
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.72721732
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2333780
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6854.5702
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: 1.94→1.99 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.307 58
Rwork0.18 1445

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