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- PDB-4p5e: CRYSTAL STRUCTURE OF HUMAN DNPH1 (RCL) WITH 6-NAPHTHYL-PURINE-RIB... -

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Basic information

Entry
Database: PDB / ID: 4p5e
TitleCRYSTAL STRUCTURE OF HUMAN DNPH1 (RCL) WITH 6-NAPHTHYL-PURINE-RIBOSIDE-MONOPHOSPHATE
Components2'-deoxynucleoside 5'-phosphate N-hydrolase 1
KeywordsHYDROLASE / RCL / DNPH1 / Inhibitor / Rossmann Fold
Function / homology
Function and homology information


deoxyribonucleoside 5'-monophosphate N-glycosidase activity / deoxyribonucleoside monophosphate catabolic process / purine nucleotide catabolic process / nucleoside salvage / Purine catabolism / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / epithelial cell differentiation / positive regulation of cell growth / protein homodimerization activity / extracellular exosome ...deoxyribonucleoside 5'-monophosphate N-glycosidase activity / deoxyribonucleoside monophosphate catabolic process / purine nucleotide catabolic process / nucleoside salvage / Purine catabolism / 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 / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsPadilla, A. / Labesse, G. / Kaminski, P.A.
Funding support France, 1items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural BiologyANR-10-INSB-05-01 France
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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3735
Polymers34,4172
Non-polymers9573
Water6,972387
1
B: 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)35,3735
Polymers34,4172
Non-polymers9573
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2990 Å2
ΔGint-39 kcal/mol
Surface area11800 Å2
MethodPISA
2
A: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)35,3735
Polymers34,4172
Non-polymers9573
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area2990 Å2
ΔGint-39 kcal/mol
Surface area11800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.974, 52.284, 54.454
Angle α, β, γ (deg.)90.00, 104.77, 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: 17208.322 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNPH1, C6orf108, RCL / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): Bli5
References: UniProt: O43598, 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 1.96 Å3/Da / Density % sol: 37.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG3K, 200 MM CALCIUM ACETATE, 100 MM TRIS, PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.8103 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8103 Å / Relative weight: 1
ReflectionResolution: 1.35→47.36 Å / Num. obs: 58489 / % possible obs: 100 % / Redundancy: 4.5 % / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 9.5
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FYI

4fyi


Resolution: 1.35→47.357 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1804 2957 5.06 %
Rwork0.155 --
obs0.1563 58476 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→47.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2200 0 65 387 2652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092473
X-RAY DIFFRACTIONf_angle_d1.3113357
X-RAY DIFFRACTIONf_dihedral_angle_d17.339937
X-RAY DIFFRACTIONf_chiral_restr0.064365
X-RAY DIFFRACTIONf_plane_restr0.007435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.37210.25991450.21822644X-RAY DIFFRACTION100
1.3721-1.39580.23271530.22722589X-RAY DIFFRACTION100
1.3958-1.42120.25021180.20232637X-RAY DIFFRACTION100
1.4212-1.44850.23961330.20122632X-RAY DIFFRACTION100
1.4485-1.47810.21641410.18412654X-RAY DIFFRACTION100
1.4781-1.51020.20321490.18012615X-RAY DIFFRACTION100
1.5102-1.54540.21421670.17412608X-RAY DIFFRACTION100
1.5454-1.5840.19631410.1642644X-RAY DIFFRACTION100
1.584-1.62690.18751480.16092616X-RAY DIFFRACTION100
1.6269-1.67470.19781400.16222651X-RAY DIFFRACTION100
1.6747-1.72880.21181090.16332625X-RAY DIFFRACTION100
1.7288-1.79060.20031440.15742655X-RAY DIFFRACTION100
1.7906-1.86230.16281240.14932662X-RAY DIFFRACTION100
1.8623-1.9470.17911600.15422636X-RAY DIFFRACTION100
1.947-2.04970.19861380.14842627X-RAY DIFFRACTION100
2.0497-2.17810.20381220.14512674X-RAY DIFFRACTION100
2.1781-2.34630.1681410.14332646X-RAY DIFFRACTION100
2.3463-2.58240.16361680.14642629X-RAY DIFFRACTION100
2.5824-2.9560.17041260.14792658X-RAY DIFFRACTION100
2.956-3.7240.15141420.1362697X-RAY DIFFRACTION100
3.724-47.3860.15411480.14672720X-RAY DIFFRACTION100
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)
11.9301-0.1657-0.04161.0640.2391.097-0.03130.1595-0.1174-0.06690.01180.07080.0607-0.06250.0220.0675-0.0038-0.0040.0709-0.00390.05344.3321-1.15748.1076
21.6333-0.00680.211.02740.27091.199-0.0267-0.09650.11040.04420.0413-0.0643-0.08120.0743-0.01680.06290.0014-0.00640.0798-0.01090.0552-25.779810.390518.0236
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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