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- PDB-8rps: Crystal structure of human DNPH1 mutant- D80N bound to 5hmdUMP -

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Basic information

Entry
Database: PDB / ID: 8rps
TitleCrystal structure of human DNPH1 mutant- D80N bound to 5hmdUMP
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-HYDROXYMETHYLURIDINE-2'-DEOXY-5'-MONOPHOSPHATE / 5-hydroxymethyl-dUMP N-hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsDevi, S. / da Silva, R.G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other privateIBioIC 2021-01-01 United Kingdom
CitationJournal: Chembiochem / Year: 2024
Title: Human 2'-Deoxynucleoside 5'-Phosphate N-Hydrolase 1: The Catalytic Roles of Tyr24 and Asp80.
Authors: Carberry, A.E. / Devi, S. / Harrison, D.J. / da Silva, R.G.
History
DepositionJan 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1
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)49,2565
Polymers48,5803
Non-polymers6762
Water3,567198
1
C: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1
hetero molecules

C: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0634
Polymers32,3862
Non-polymers6762
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4040 Å2
ΔGint-34 kcal/mol
Surface area11530 Å2
MethodPISA
2
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)32,7253
Polymers32,3862
Non-polymers3381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-32 kcal/mol
Surface area11690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.879, 56.828, 88.543
Angle α, β, γ (deg.)90.00, 106.45, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 16193.235 Da / Num. of mol.: 3 / Mutation: D80N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNPH1, C6orf108, RCL / Production host: Escherichia coli (E. coli)
References: UniProt: O43598, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical ChemComp-5HU / 5-HYDROXYMETHYLURIDINE-2'-DEOXY-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 338.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N2O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.86 Å3/Da / Density % sol: 33.98 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4
Details: [25 mM sodium malonate, 37.5 mM imidazole and 37.5 mM boric acid] pH 4.0 and 15 % PEG 1500.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.6199 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 1.75→44.56 Å / Num. obs: 36132 / % possible obs: 100 % / Redundancy: 5.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.102 / Net I/σ(I): 8.4
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 2 / Num. unique obs: 1975 / CC1/2: 0.707 / Rpim(I) all: 0.65 / Rrim(I) all: 1.148 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→42.46 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2039 1815 5.03 %
Rwork0.1794 --
obs0.1806 36088 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→42.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3079 0 44 198 3321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.971
X-RAY DIFFRACTIONf_dihedral_angle_d6.542460
X-RAY DIFFRACTIONf_chiral_restr0.054460
X-RAY DIFFRACTIONf_plane_restr0.018565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80.29281380.24322565X-RAY DIFFRACTION99
1.8-1.850.27111480.22092620X-RAY DIFFRACTION100
1.85-1.910.34161380.26072607X-RAY DIFFRACTION99
1.91-1.980.22961390.20952638X-RAY DIFFRACTION100
1.98-2.060.2321160.20392660X-RAY DIFFRACTION100
2.06-2.150.2281240.19092640X-RAY DIFFRACTION100
2.15-2.260.25231500.20662612X-RAY DIFFRACTION99
2.26-2.40.2031290.17932622X-RAY DIFFRACTION100
2.4-2.590.1921740.17492629X-RAY DIFFRACTION100
2.59-2.850.22451460.1772621X-RAY DIFFRACTION100
2.85-3.260.17871390.17242653X-RAY DIFFRACTION100
3.26-4.110.17611400.15582671X-RAY DIFFRACTION100
4.11-42.460.17521340.1632735X-RAY DIFFRACTION100

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