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- PDB-4p5d: CRYSTAL STRUCTURE OF RAT DNPH1 (RCL) WITH 6-NAPHTHYL-PURINE-RIBOS... -

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Basic information

Entry
Database: PDB / ID: 4p5d
TitleCRYSTAL STRUCTURE OF RAT DNPH1 (RCL) WITH 6-NAPHTHYL-PURINE-RIBOSIDE-MONOPHOSPHATE
Components2'-deoxynucleoside 5'-phosphate N-hydrolase 1
KeywordsHYDROLASE / N-GLYCOSIDASE / INHIBITOR
Function / homology
Function and homology information


Purine catabolism / deoxyribonucleoside monophosphate catabolic process / 5-hydroxymethyl-dUMP N-hydrolase activity / nucleoside salvage / dGMP catabolic process / allantoin metabolic process / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / epithelial cell differentiation / positive regulation of cell growth / protein homodimerization activity ...Purine catabolism / deoxyribonucleoside monophosphate catabolic process / 5-hydroxymethyl-dUMP N-hydrolase activity / nucleoside salvage / dGMP catabolic process / allantoin metabolic process / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / epithelial cell differentiation / positive regulation of cell growth / protein homodimerization activity / identical protein binding / nucleus / cytoplasm
Similarity search - Function
2-deoxynucleoside 5-phosphate N-hydrolase 1, DNPH1 / : / Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-N6P / 5-hydroxymethyl-dUMP N-hydrolase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsPadilla, A. / Labesse, G. / Kaminski, P.A.
Citation
Journal: Eur.J.Med.Chem. / Year: 2014
Title: 6-(Hetero)Arylpurine nucleotides as inhibitors of the oncogenic target DNPH1: Synthesis, structural studies and cytotoxic activities.
Authors: Amiable, C. / Paoletti, J. / Haouz, A. / Padilla, A. / Labesse, G. / Kaminski, P.A. / Pochet, S.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2013
Title: Structure of the oncoprotein Rcl bound to three nucleotide analogues.
Authors: Padilla, A. / Amiable, C. / Pochet, S. / Kaminski, P.A. / Labesse, G.
History
DepositionMar 16, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)35,3595
Polymers34,3472
Non-polymers1,0133
Water2,594144
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)35,2634
Polymers34,3472
Non-polymers9172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_554-x+y,y,-z-1/21
Buried area3090 Å2
ΔGint-32 kcal/mol
Surface area12070 Å2
MethodPISA
2
A: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)35,4566
Polymers34,3472
Non-polymers1,1094
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-2/31
Buried area3300 Å2
ΔGint-43 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.200, 178.200, 56.922
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-346-

HOH

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Components

#1: Protein 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 / Deoxyribonucleoside 5'-monophosphate N-glycosidase / c-Myc-responsive protein Rcl


Mass: 17173.334 Da / Num. of mol.: 2 / Fragment: Residues 11-151 / Mutation: yes
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dnph1, Rcl / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): Bli5
References: UniProt: O35820, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical ChemComp-N6P / 6-(naphthalen-2-yl)-9-(5-O-phosphono-beta-D-ribofuranosyl)-9H-purine / 6-Naphthylpurine riboside 5'-monophosphate


Mass: 458.361 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H19N4O7P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 67.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.3 M LITHIUM SULFATE, 1% PEG2K, 20 MM MAGNESIUM SULFATE, 100 MM TRIS, PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9793 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.109→38.59 Å / Num. obs: 31129 / % possible obs: 99.4 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.9
Reflection shellResolution: 2.11→2.22 Å / % possible obs: 99.5 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
MOSFLMdata reduction
SCALA3.3.15data scaling
MOLREP10.2.31phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FYI

4fyi


Resolution: 2.11→38.165 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 18.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1978 1560 5.06 %random
Rwork0.1746 ---
obs0.1757 30858 99.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.11→38.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2246 0 69 144 2459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092408
X-RAY DIFFRACTIONf_angle_d1.433271
X-RAY DIFFRACTIONf_dihedral_angle_d17.708869
X-RAY DIFFRACTIONf_chiral_restr0.061347
X-RAY DIFFRACTIONf_plane_restr0.007423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1094-2.17750.23471460.21852600X-RAY DIFFRACTION99
2.1775-2.25530.25641350.21792617X-RAY DIFFRACTION99
2.2553-2.34560.22261430.19142609X-RAY DIFFRACTION99
2.3456-2.45230.24671350.19042613X-RAY DIFFRACTION98
2.4523-2.58160.20961250.18462639X-RAY DIFFRACTION99
2.5816-2.74330.20511550.18512630X-RAY DIFFRACTION99
2.7433-2.9550.21821380.18462659X-RAY DIFFRACTION100
2.955-3.25230.22781350.17742664X-RAY DIFFRACTION99
3.2523-3.72260.19461580.17032668X-RAY DIFFRACTION99
3.7226-4.68870.14431400.13942735X-RAY DIFFRACTION99
4.6887-38.17170.19811500.17972864X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1131-0.644-0.11183.35750.25472.6638-0.0716-0.76250.17450.4101-0.0454-0.0493-0.19940.18150.10780.2138-0.0147-0.03270.7188-0.0280.2999-0.604773.3697-2.5077
22.27380.4416-0.32083.86150.03534.2026-0.0209-0.42160.12010.50340.0597-0.04890.25780.024-0.03260.21330.085-0.02920.3297-0.01950.212436.071763.9842-7.1982
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain C and resseq 10:151)
2X-RAY DIFFRACTION2(chain A and resseq 10:152)

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