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- PDB-4nfl: Crystal structure of human mitochondrial 5'(3')-deoxyribonucleoti... -

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Basic information

Entry
Database: PDB / ID: 4nfl
TitleCrystal structure of human mitochondrial 5'(3')-deoxyribonucleotidase in complex with the inhibitor NPB-T
Components5'(3')-deoxyribonucleotidase, mitochondrial
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HAD-like / nucleotidase / mitochondria / HYDROLASE-HYDROLASE INHIBITOR complex
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
Chem-2JW / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / 5'(3')-deoxyribonucleotidase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.375 Å
AuthorsPachl, P. / Rezacova, P. / Brynda, J.
CitationJournal: Org.Biomol.Chem. / Year: 2014
Title: Conformationally constrained nucleoside phosphonic acids - potent inhibitors of human mitochondrial and cytosolic 5'(3')-nucleotidases.
Authors: Simak, O. / Pachl, P. / Fabry, M. / Budesinsky, M. / Jandusik, T. / Hnizda, A. / Sklenickova, R. / Petrova, M. / Veverka, V. / Rezacova, P. / Brynda, J. / Rosenberg, I.
History
DepositionOct 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,25319
Polymers23,1681
Non-polymers2,08418
Water5,260292
1
A: 5'(3')-deoxyribonucleotidase, mitochondrial
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)50,50538
Polymers46,3372
Non-polymers4,16836
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area10580 Å2
ΔGint-14 kcal/mol
Surface area17600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.650, 73.650, 105.910
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-484-

HOH

21A-575-

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: 23168.391 Da / Num. of mol.: 1 / Fragment: UNP residues 32-227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NT5M, DNT2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NPB1, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases

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Non-polymers , 7 types, 310 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-2JW / 1-{2-deoxy-3,5-O-[(4-nitrophenyl)(phosphono)methylidene]-beta-D-threo-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione


Mass: 455.313 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18N3O10P
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 3.1 Å3/Da / Density % sol: 60.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 20 mM potassium phosphate monobasic, 8% PEG8000, 10% glycerol, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: 1.375→52.078 Å / Num. obs: 56940 / % possible obs: 90.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.35 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 26.11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.375-1.450.6741.9126774617661.9
1.45-1.550.4044.1348600806586.1
1.55-1.670.238.8371625875799.8
1.67-1.830.12815.3167365806399.6
1.83-2.050.06627.3461312730799.2
2.05-2.360.0442.3154343644398.7
2.36-2.890.03254.9745929544597.9
2.89-4.080.02768.6335350424696.6
4.080.02672.8519342243794.4

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Processing

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

4l6a


Resolution: 1.375→46.73 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.1674 / WRfactor Rwork: 0.1463 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8897 / SU B: 1.57 / SU ML: 0.033 / SU R Cruickshank DPI: 0.0474 / SU Rfree: 0.0502 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.176 2886 5.1 %RANDOM
Rwork0.1526 ---
obs0.1538 56839 92.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.24 Å2 / Biso mean: 22.2308 Å2 / Biso min: 8.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0 Å2
2---0.11 Å2-0 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.375→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1633 0 123 292 2048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021876
X-RAY DIFFRACTIONr_bond_other_d0.0030.021776
X-RAY DIFFRACTIONr_angle_refined_deg2.0442.0152538
X-RAY DIFFRACTIONr_angle_other_deg0.9553.0044108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0065224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.93323.18288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.73315302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.021515
X-RAY DIFFRACTIONr_chiral_restr0.1060.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212030
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02435
X-RAY DIFFRACTIONr_mcbond_it1.6271.495831
X-RAY DIFFRACTIONr_mcbond_other1.6261.496832
X-RAY DIFFRACTIONr_mcangle_it2.6022.2321044
LS refinement shellResolution: 1.375→1.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 146 -
Rwork0.261 2516 -
all-2662 -
obs--60.02 %
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)
10.6208-0.34931.58580.208-0.89834.05550.141-0.0954-0.0545-0.10030.02130.03390.3859-0.2296-0.16230.0916-0.00280.03580.0624-0.0140.0896-4.1839-0.29514.1889
20.4871-0.1222-0.15150.55010.2110.110.0217-0.00140.0552-0.02980.0119-0.0693-0.0158-0.0069-0.03350.02150.00190.02030.0239-0.00410.0301-7.255226.031720.0036
30.61050.2814-0.25570.23820.05040.3883-0.0011-0.0286-0.1076-0.01690.0027-0.0957-0.01430.0462-0.00160.00790.00430.01980.02260.01010.06874.727813.751718.794
42.27664.17031.31917.65652.43480.79780.0792-0.0372-0.17240.1369-0.0632-0.27870.0554-0.0298-0.01610.04590.00430.04280.0563-0.01510.2384-3.834624.837428.6956
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 39
2X-RAY DIFFRACTION2A40 - 159
3X-RAY DIFFRACTION3A160 - 227
4X-RAY DIFFRACTION4A303

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