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- PDB-4l6a: Structure of human mitochondrial 5'(3')-deoxyribonucleotidase -

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Basic information

Entry
Database: PDB / ID: 4l6a
TitleStructure of human mitochondrial 5'(3')-deoxyribonucleotidase
Components5'(3')-deoxyribonucleotidase, mitochondrial
KeywordsHYDROLASE / PROTEIN CONFORMATION / SEQUENCE HOMOLOGY / HAD-LIKE / DEPHOSPHORYLATION / PHOSPHORYLATION
Function / homology
Function and homology information


pyrimidine deoxyribonucleotide catabolic process / nucleotidase activity / dUMP catabolic process / Pyrimidine catabolism / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsPachl, P. / Brynda, J. / Rezacova, P.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2014
Title: Structures of human cytosolic and mitochondrial nucleotidases: implications for structure-based design of selective inhibitors.
Authors: Pachl, P. / Fabry, M. / Rosenberg, I. / Simak, O. / Rezacova, P. / Brynda, J.
History
DepositionJun 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 28, 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_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: 5'(3')-deoxyribonucleotidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,68317
Polymers23,2721
Non-polymers1,41216
Water5,621312
1
A: 5'(3')-deoxyribonucleotidase, mitochondrial
hetero molecules

A: 5'(3')-deoxyribonucleotidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,36634
Polymers46,5432
Non-polymers2,82332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area9750 Å2
ΔGint-40 kcal/mol
Surface area18240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.410, 73.410, 106.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-695-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 5'(3')-deoxyribonucleotidase, mitochondrial / 5' / 3'-nucleotidase / mitochondrial / Deoxy-5'-nucleotidase 2 / dNT-2


Mass: 23271.533 Da / Num. of mol.: 1 / Fragment: UNP residues 32-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNT2, NT5M / Plasmid: PMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9NPB1, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases

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Non-polymers , 6 types, 328 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 / Phosphate


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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 3.09 Å3/Da / Density % sol: 60.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 8% PEG 8000, 20MM POTASSIUM PHOSPHATE, 10% GLYCEROL, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91502 / Wavelength: 1.255 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.915021
21.2551
ReflectionResolution: 1.4→25.498 Å / Num. obs: 57600 / Redundancy: 5 % / Rsym value: 0.063 / Net I/σ(I): 11.9
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.472

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.4→25.498 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.219 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.154 2902 5 %RANDOM
Rwork0.141 ---
obs0.141 57598 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: 18.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.4→25.498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1636 0 80 312 2028
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021848
X-RAY DIFFRACTIONr_bond_other_d0.0030.021365
X-RAY DIFFRACTIONr_angle_refined_deg2.0871.9932498
X-RAY DIFFRACTIONr_angle_other_deg1.0143.0023277
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0825228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.3852390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.02415313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0981517
X-RAY DIFFRACTIONr_chiral_restr0.1090.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211999
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02402
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 190 -
Rwork0.255 3693 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3461-0.7567-0.56181.5880.37180.76580.0628-0.09340.2278-0.07020.0334-0.2297-0.12630.0364-0.09620.0272-0.00950.01620.0222-0.01410.0516-4.33629.39322.225
20.76630.1223-0.27250.5064-0.04720.5475-0.02150.0057-0.0859-0.0519-0.0042-0.08730.01180.03240.02570.0137-0.00210.01760.0157-0.00050.0289-1.99414.61317.566
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 100
2X-RAY DIFFRACTION2A101 - 221

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