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- PDB-4l57: High resolutin structure of human cytosolic 5'(3')-deoxyribonucle... -

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Basic information

Entry
Database: PDB / ID: 4l57
TitleHigh resolutin structure of human cytosolic 5'(3')-deoxyribonucleotidase
Components5'(3')-deoxyribonucleotidase, cytosolic type
KeywordsHYDROLASE / 5'-NUCLEOTIDASE / PROTEIN CONFORMATION / SEQUENCE HOMOLOGY / HAD-LIKE / DEPHOSPHORYLATION
Function / homology
Function and homology information


pyrimidine nucleotide binding / dTMP catabolic process / pyrimidine deoxyribonucleotide catabolic process / dCMP catabolic process / dGMP catabolic process / UMP catabolic process / nucleotidase activity / amide catabolic process / dUMP catabolic process / Pyrimidine catabolism ...pyrimidine nucleotide binding / dTMP catabolic process / pyrimidine deoxyribonucleotide catabolic process / dCMP catabolic process / dGMP catabolic process / UMP catabolic process / nucleotidase activity / amide catabolic process / dUMP catabolic process / Pyrimidine catabolism / IMP 5'-nucleotidase activity / IMP catabolic process / Purine catabolism / allantoin metabolic process / 5'-nucleotidase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / dephosphorylation / extracellular exosome / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm
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
PHOSPHATE ION / 5'(3')-deoxyribonucleotidase, cytosolic type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.08 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 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Refinement description
Revision 1.2Apr 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 1.3Feb 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_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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_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_asym_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_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, cytosolic type
B: 5'(3')-deoxyribonucleotidase, cytosolic type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,42413
Polymers45,6102
Non-polymers81411
Water7,981443
1
A: 5'(3')-deoxyribonucleotidase, cytosolic type
hetero molecules

B: 5'(3')-deoxyribonucleotidase, cytosolic type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,42413
Polymers45,6102
Non-polymers81411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area4700 Å2
ΔGint-62 kcal/mol
Surface area17750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.128, 46.493, 61.409
Angle α, β, γ (deg.)68.16, 81.47, 75.28
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 5'(3')-deoxyribonucleotidase, cytosolic type / Cytosolic 5' / 3'-pyrimidine nucleotidase / Deoxy-5'-nucleotidase 1 / dNT-1


Mass: 22805.162 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNT1, NT5C, UMPH2 / Plasmid: pET 22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8TCD5, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases

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Non-polymers , 5 types, 454 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.19 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 291 K / pH: 4.2
Details: 40MM KH2PO4, 5% PEG 8000, 20% GLYCEROL, pH 4.2, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.08→23.4 Å / Num. all: 144252 / Num. obs: 142636 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassificationNB
SHELXrefinement
PDB_EXTRACT3.11data extraction
SHELXLrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.08→22.48 Å / Occupancy max: 1 / Occupancy min: 0.01
RfactorNum. reflection
Rfree0.183 1463
Rwork0.1436 -
obs0.1436 142636
all-144252
Displacement parametersBiso max: 126.51 Å2 / Biso mean: 16.1068 Å2 / Biso min: 5.58 Å2
Refinement stepCycle: LAST / Resolution: 1.08→22.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3163 0 49 443 3655

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