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- PDB-8os9: Structure of Homo sapiens 2'-deoxynucleoside 5'-phosphate N-hydro... -

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Basic information

Entry
Database: PDB / ID: 8os9
TitleStructure of Homo sapiens 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 (DNPH1)
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 / cytoplasm / cytosol
Similarity search - Function
2-deoxynucleoside 5-phosphate N-hydrolase 1, DNPH1 / : / Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase
Similarity search - Domain/homology
5-hydroxymethyl-dUMP N-hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
C: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1
D: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1


Theoretical massNumber of molelcules
Total (without water)64,7774
Polymers64,7774
Non-polymers00
Water2,954164
1
A: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1
D: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1


Theoretical massNumber of molelcules
Total (without water)32,3882
Polymers32,3882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-28 kcal/mol
Surface area11690 Å2
MethodPISA
2
B: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1
C: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1


Theoretical massNumber of molelcules
Total (without water)32,3882
Polymers32,3882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-28 kcal/mol
Surface area11670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.491, 64.517, 62.939
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 4
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 1.8 Å3/Da / Density % sol: 31.76 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting 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: Jul 22, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.7→62.93 Å / Num. obs: 45873 / % possible obs: 90.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 30.42 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.018 / Rrim(I) all: 0.048 / Net I/σ(I): 18.3
Reflection shellResolution: 1.7→1.729 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2455 / CC1/2: 0.853 / Rpim(I) all: 0.261 / Rrim(I) all: 0.664 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→45.05 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2299 2312 5.04 %
Rwork0.2032 --
obs0.2047 45838 90.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→45.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3884 0 0 164 4048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.989
X-RAY DIFFRACTIONf_dihedral_angle_d6.378566
X-RAY DIFFRACTIONf_chiral_restr0.057581
X-RAY DIFFRACTIONf_plane_restr0.015708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.33451420.2862785X-RAY DIFFRACTION99
1.73-1.770.28891740.26482756X-RAY DIFFRACTION99
1.77-1.810.27361570.24382802X-RAY DIFFRACTION100
1.81-1.860.26031490.22072831X-RAY DIFFRACTION100
1.86-1.910.26951210.21512853X-RAY DIFFRACTION100
1.91-1.970.28691580.22242776X-RAY DIFFRACTION100
1.97-2.030.291450.23092841X-RAY DIFFRACTION100
2.03-2.10.2805160.2388578X-RAY DIFFRACTION20
2.1-2.190.22781450.21982856X-RAY DIFFRACTION100
2.19-2.280.2107910.22721854X-RAY DIFFRACTION66
2.28-2.410.27951390.22112851X-RAY DIFFRACTION100
2.41-2.560.26961590.21332826X-RAY DIFFRACTION100
2.56-2.750.2601960.23372224X-RAY DIFFRACTION77
2.75-3.030.22821790.21772802X-RAY DIFFRACTION100
3.03-3.410.26481050.19642579X-RAY DIFFRACTION100
3.48-4.370.20291460.17452448X-RAY DIFFRACTION88
4.37-45.050.19511900.18322864X-RAY DIFFRACTION99

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