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- PDB-8osc: Structure of Homo sapiens 2'-deoxynucleoside 5'-phosphate N-hydro... -

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Basic information

Entry
Database: PDB / ID: 8osc
TitleStructure of Homo sapiens 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 (DNPH1) bound to deoxyuridine 5'- monophosphate
Components2'-deoxynucleoside 5'-phosphate N-hydrolase 1
KeywordsHYDROLASE / deoxyribonucleoside 5'-monophosphate N-glycosidase activity
Function / homology
Function and homology information


purine nucleotide catabolic process / deoxyribonucleoside monophosphate catabolic process / 5-hydroxymethyl-dUMP N-hydrolase activity / nucleoside salvage / dGMP catabolic process / Purine catabolism / allantoin metabolic process / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / epithelial cell differentiation / positive regulation of cell growth ...purine nucleotide catabolic process / deoxyribonucleoside monophosphate catabolic process / 5-hydroxymethyl-dUMP N-hydrolase activity / nucleoside salvage / dGMP catabolic process / Purine catabolism / allantoin metabolic process / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / epithelial cell differentiation / positive regulation of cell growth / protein homodimerization activity / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
2-deoxynucleoside 5-phosphate N-hydrolase 1, DNPH1 / : / Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase
Similarity search - Domain/homology
2'-DEOXYURIDINE 5'-MONOPHOSPHATE / 5-hydroxymethyl-dUMP N-hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsDevi, S. / da Silva, R.G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other privateIBioIC 2021-01-01 United Kingdom
CitationJournal: Biochemistry / Year: 2023
Title: Human 2'-Deoxynucleoside 5'-Phosphate N -Hydrolase 1: Mechanism of 2'-Deoxyuridine 5'-Monophosphate Hydrolysis.
Authors: Devi, S. / Carberry, A.E. / Zickuhr, G.M. / Dickson, A.L. / Harrison, D.J. / da Silva, R.G.
History
DepositionApr 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1
B: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6973
Polymers32,3882
Non-polymers3081
Water3,459192
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-34 kcal/mol
Surface area11190 Å2
Unit cell
Length a, b, c (Å)107.354, 38.772, 66.195
Angle α, β, γ (deg.)90.00, 120.29, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-315-

HOH

21B-371-

HOH

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Components

#1: Protein 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 / c-Myc-responsive protein RCL


Mass: 16194.220 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNPH1, C6orf108, RCL / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: O43598, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.84 Å3/Da / Density % sol: 33.04 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4
Details: [40 mM sodium propionate, 20 mM MES and 40 mM BIS-TRIS propane] pH 4.0 and 20% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 8, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.42→33.38 Å / Num. obs: 44559 / % possible obs: 99.7 % / Redundancy: 15.4 % / Biso Wilson estimate: 19.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.015 / Rrim(I) all: 0.06 / Net I/σ(I): 24.7
Reflection shellResolution: 1.42→1.44 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.814 / Mean I/σ(I) obs: 4 / Num. unique obs: 2097 / CC1/2: 0.899 / Rpim(I) all: 0.254 / Rrim(I) all: 0.855 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→33.38 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 21.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2104 2299 5.16 %
Rwork0.1972 --
obs0.1979 44541 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.42→33.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 0 20 192 2163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.941
X-RAY DIFFRACTIONf_dihedral_angle_d15.603291
X-RAY DIFFRACTIONf_chiral_restr0.078293
X-RAY DIFFRACTIONf_plane_restr0.009354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.450.27681330.24892494X-RAY DIFFRACTION95
1.45-1.480.26411270.21912638X-RAY DIFFRACTION100
1.48-1.520.26231450.222617X-RAY DIFFRACTION100
1.52-1.560.2251480.21872636X-RAY DIFFRACTION100
1.56-1.610.26191430.2112613X-RAY DIFFRACTION100
1.61-1.660.23171420.21442646X-RAY DIFFRACTION100
1.66-1.720.23631390.21992650X-RAY DIFFRACTION100
1.72-1.790.2351340.21452657X-RAY DIFFRACTION100
1.79-1.870.24131390.20832631X-RAY DIFFRACTION100
1.87-1.970.23031690.19782615X-RAY DIFFRACTION100
1.97-2.090.2141570.19682624X-RAY DIFFRACTION100
2.09-2.250.18871390.19292663X-RAY DIFFRACTION100
2.25-2.480.2281470.19462668X-RAY DIFFRACTION100
2.48-2.840.21521320.2022670X-RAY DIFFRACTION100
2.84-3.580.221490.18872681X-RAY DIFFRACTION100
3.58-33.380.17641560.18832739X-RAY DIFFRACTION100

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