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- PDB-4mum: Crystal structure of mitochondrial 5'(3')-deoxy ribonucleotidase ... -

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Basic information

Entry
Database: PDB / ID: 4mum
TitleCrystal structure of mitochondrial 5'(3')-deoxy ribonucleotidase alternative spliced variant
ComponentsMitochondrial 5' nucleotidase
KeywordsHYDROLASE / 5'-nucleotidase / protein conformation / sequence homology / HAD-like / dephosphorylation
Function / homology
Function and homology information


pyrimidine deoxyribonucleotide catabolic process / nucleotidase activity / dUMP catabolic process / Pyrimidine catabolism / deoxyribonucleotide catabolic process / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / 5'-nucleotidase activity / DNA replication / mitochondrial matrix / nucleotide binding ...pyrimidine deoxyribonucleotide catabolic process / nucleotidase activity / dUMP catabolic process / Pyrimidine catabolism / deoxyribonucleotide catabolic process / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / 5'-nucleotidase activity / DNA replication / mitochondrial matrix / nucleotide binding / mitochondrion / metal ion binding
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
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / 5'(3')-deoxyribonucleotidase, mitochondrial / 5'(3')-deoxyribonucleotidase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.271 Å
AuthorsPachl, P. / Rezacova, P.
CitationJournal: J Enzyme Inhib Med Chem / Year: 2015
Title: Kinetic and structural characterization of an alternatively spliced variant of human mitochondrial 5'(3')-deoxyribonucleotidase.
Authors: Pachl, P. / Fabry, M. / Veverka, V. / Brynda, J. / Rezacova, P.
History
DepositionSep 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
Revision 1.2Sep 20, 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_ref_seq_dif / 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_ref_seq_dif.details / _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: Mitochondrial 5' nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,23016
Polymers23,8101
Non-polymers1,42015
Water5,188288
1
A: Mitochondrial 5' nucleotidase
hetero molecules

A: Mitochondrial 5' nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,46032
Polymers47,6202
Non-polymers2,84030
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area9840 Å2
ΔGint-68 kcal/mol
Surface area17270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.372, 73.372, 106.672
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-579-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Mitochondrial 5' nucleotidase / 5'(3')-deoxyribonucleotidase


Mass: 23810.129 Da / Num. of mol.: 1 / Fragment: UNP residues 32-233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNT1, NT5C, UMPH2 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2I378, UniProt: Q9NPB1*PLUS, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases

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Non-polymers , 8 types, 303 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 3.01 Å3/Da / Density % sol: 59.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 20 mM potassium phosphate monobasic, 8% PEG8000, 10% gycerol, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.97826 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 31, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97826 Å / Relative weight: 1
ReflectionResolution: 1.271→46.656 Å / Num. obs: 76192 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.812 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 26.48
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.271-1.350.6082.053855711389192.7
1.35-1.440.4074.366718511569199.9
1.44-1.560.2358.878654107821100
1.56-1.70.12715.477319699771100
1.7-1.910.06826.716663890471100
1.91-2.20.03744.35925680341100
2.2-2.690.02761.625003668551100
2.69-3.80.02276.43859353881100
3.8-46.6560.0283.54211773151199.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4L6A

4l6a


Resolution: 1.271→46.656 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / WRfactor Rfree: 0.1403 / WRfactor Rwork: 0.1245 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9277 / SU B: 0.975 / SU ML: 0.019 / SU R Cruickshank DPI: 0.0336 / SU Rfree: 0.0329 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1492 3809 5 %RANDOM
Rwork0.1312 ---
obs0.1321 76191 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.06 Å2 / Biso mean: 18.6249 Å2 / Biso min: 8.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2--0.33 Å2-0 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.271→46.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1607 0 77 288 1972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191837
X-RAY DIFFRACTIONr_bond_other_d0.0010.021762
X-RAY DIFFRACTIONr_angle_refined_deg2.3361.9932489
X-RAY DIFFRACTIONr_angle_other_deg2.07734074
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.015226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.74523.05985
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.42315306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7421515
X-RAY DIFFRACTIONr_chiral_restr0.1430.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212001
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02422
X-RAY DIFFRACTIONr_mcbond_it0.7961.516836
X-RAY DIFFRACTIONr_mcbond_other0.7971.516837
X-RAY DIFFRACTIONr_mcangle_it1.1242.2631049
X-RAY DIFFRACTIONr_rigid_bond_restr7.61933596
X-RAY DIFFRACTIONr_sphericity_free28.047570
X-RAY DIFFRACTIONr_sphericity_bonded8.70853777
LS refinement shellResolution: 1.271→1.304 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 248 -
Rwork0.238 4670 -
all-4918 -
obs--87.56 %

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