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- PDB-8rpt: Crystal structure of human DNPH1 mutant- D80A -

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Basic information

Entry
Database: PDB / ID: 8rpt
TitleCrystal structure of human DNPH1 mutant- D80A
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
DI(HYDROXYETHYL)ETHER / 5-hydroxymethyl-dUMP N-hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
B: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1
A: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,04516
Polymers32,3002
Non-polymers74414
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-95 kcal/mol
Surface area12820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.481, 65.584, 69.209
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 16150.210 Da / Num. of mol.: 2 / Mutation: D80A
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 1.98 Å3/Da / Density % sol: 37.96 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 8 % PEG 4000, 100 mM Sodium acetate pH 4.6

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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: Dec 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 1.95→47.64 Å / Num. obs: 19407 / % possible obs: 100 % / Redundancy: 16.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.182 / Rrim(I) all: 0.193 / Net I/σ(I): 11.8
Reflection shellResolution: 1.95→2 Å / Redundancy: 17.5 % / Rmerge(I) obs: 1.476 / Num. unique obs: 1320 / CC1/2: 0.836 / R split: 2.4 / Rpim(I) all: 0.52 / % 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: 1.95→47.6 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2195 936 4.84 %
Rwork0.1778 --
obs0.1798 19353 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2137 0 38 145 2320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.871
X-RAY DIFFRACTIONf_dihedral_angle_d8.901333
X-RAY DIFFRACTIONf_chiral_restr0.055323
X-RAY DIFFRACTIONf_plane_restr0.012400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.050.2961370.2242536X-RAY DIFFRACTION99
2.05-2.180.26571600.1972578X-RAY DIFFRACTION100
2.18-2.350.23261320.17742585X-RAY DIFFRACTION100
2.35-2.580.23551180.18452626X-RAY DIFFRACTION100
2.58-2.960.22621270.18512631X-RAY DIFFRACTION100
2.96-3.720.20681590.16222641X-RAY DIFFRACTION100
3.73-47.60.18491030.17152820X-RAY DIFFRACTION100

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