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- PDB-8rqd: Crystal structure of human DNPH1 mutant-Y24F -

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Basic information

Entry
Database: PDB / ID: 8rqd
TitleCrystal structure of human DNPH1 mutant-Y24F
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
DI(HYDROXYETHYL)ETHER / 5-hydroxymethyl-dUMP N-hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,23113
Polymers32,3562
Non-polymers87511
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-50 kcal/mol
Surface area12840 Å2
Unit cell
Length a, b, c (Å)139.907, 139.907, 33.313
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 16178.220 Da / Num. of mol.: 2 / Mutation: Y24F
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.: 4 / 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.: 6 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 1.94 Å3/Da / Density % sol: 36.63 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1 M MES pH 6.5 30 % PEG 5000 MME

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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: 2.14→70.03 Å / Num. obs: 13475 / % possible obs: 100 % / Redundancy: 10.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.088 / Rrim(I) all: 0.206 / Net I/σ(I): 7.7
Reflection shellResolution: 2.14→2.2 Å / Redundancy: 10.3 % / Rmerge(I) obs: 1.028 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1129 / CC1/2: 0.885 / Rpim(I) all: 0.493 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→40.42 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.342 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.309 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23697 721 5.4 %RANDOM
Rwork0.17852 ---
obs0.18191 12741 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.809 Å2
Baniso -1Baniso -2Baniso -3
1--2.1 Å2-1.05 Å20 Å2
2---2.1 Å20 Å2
3---6.8 Å2
Refinement stepCycle: 1 / Resolution: 2.14→40.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2183 0 51 44 2278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122264
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162171
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.8473029
X-RAY DIFFRACTIONr_angle_other_deg0.5461.7634943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4125273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.056534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59310375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0710.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022797
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02599
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.083.2811099
X-RAY DIFFRACTIONr_mcbond_other3.0793.2821100
X-RAY DIFFRACTIONr_mcangle_it4.6775.8751369
X-RAY DIFFRACTIONr_mcangle_other4.6775.8761370
X-RAY DIFFRACTIONr_scbond_it4.3313.8841165
X-RAY DIFFRACTIONr_scbond_other4.2043.8911162
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4876.8351655
X-RAY DIFFRACTIONr_long_range_B_refined9.00539.822590
X-RAY DIFFRACTIONr_long_range_B_other9.00139.812588
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.14→2.193 Å
RfactorNum. reflection% reflection
Rfree0.304 57 -
Rwork0.288 945 -
obs--99.9 %

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