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- PDB-1q92: Crystal structure of human mitochondrial deoxyribonucleotidase in... -

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Basic information

Entry
Database: PDB / ID: 1q92
TitleCrystal structure of human mitochondrial deoxyribonucleotidase in complex with the inhibitor PMcP-U
Components5(3)-deoxyribonucleotidase
KeywordsHYDROLASE / alpha-beta rossman fold
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-DRM / 5'(3')-deoxyribonucleotidase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsRinaldo-Matthis, A. / Rampazzo, C. / Balzarini, J. / Reichard, P. / Bianchi, V. / Nordlund, P.
CitationJournal: Mol.Pharmacol. / Year: 2004
Title: Crystal structures of the mitochondrial deoxyribonucleotidase in complex with two specific inhibitors
Authors: Rinaldo-Matthis, A. / Rampazzo, C. / Balzarini, J. / Reichard, P. / Bianchi, V. / Nordlund, P.
History
DepositionAug 22, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,2484
Polymers22,8411
Non-polymers4073
Water5,873326
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.758, 73.758, 105.981
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein 5(3)-deoxyribonucleotidase / deoxyribonucleotidase


Mass: 22841.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NPB1, 5'-nucleotidase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DRM / {[(1R,2S)-2-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)CYCLOPENTYL]OXY}METHYLPHOSPHONIC ACID / 1-TRANS-(2-PHOSPHONOMETHOXYCYCLOPENTYL)URACIL / PMCP-U


Type: DNA linking / Mass: 290.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O6P
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.63 Å3/Da / Density % sol: 52.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: PEG 8000, potassium phosphate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. all: 209551 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.4→1.45 Å

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1MH9

1mh9


Resolution: 1.4→25.32 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.982 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16454 1929 5.1 %RANDOM
Rwork0.13337 ---
obs0.13503 35599 64.83 %-
all-37528 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.719 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.4→25.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1602 0 26 326 1954
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221659
X-RAY DIFFRACTIONr_bond_other_d0.0020.021489
X-RAY DIFFRACTIONr_angle_refined_deg1.8561.9632223
X-RAY DIFFRACTIONr_angle_other_deg1.00833466
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3255178
X-RAY DIFFRACTIONr_chiral_restr0.1320.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021726
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02355
X-RAY DIFFRACTIONr_nbd_refined0.5010.2413
X-RAY DIFFRACTIONr_nbd_other0.2520.21635
X-RAY DIFFRACTIONr_nbtor_other0.0860.2933
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2490.2239
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3010.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3850.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.290.226
X-RAY DIFFRACTIONr_mcbond_it1.731.5962
X-RAY DIFFRACTIONr_mcangle_it2.58621534
X-RAY DIFFRACTIONr_scbond_it3.3043697
X-RAY DIFFRACTIONr_scangle_it4.7974.5689
X-RAY DIFFRACTIONr_rigid_bond_restr1.94721659
X-RAY DIFFRACTIONr_sphericity_free5.482327
X-RAY DIFFRACTIONr_sphericity_bonded3.82221627
LS refinement shellResolution: 1.402→1.439 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.133 35
Rwork0.093 573

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