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- PDB-4kxm: Crystal structure of DNPH1 (RCL) WITH N6-ISOPENTENYL-AMP -

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Basic information

Entry
Database: PDB / ID: 4kxm
TitleCrystal structure of DNPH1 (RCL) WITH N6-ISOPENTENYL-AMP
Components2'-deoxynucleoside 5'-phosphate N-hydrolase 1
KeywordsHYDROLASE / DEOXYRIBONUCLEOSIDE 5'-MONOPHOSPHATE N-GLYCOSIDASE
Function / homology
Function and homology information


Purine catabolism / deoxyribonucleoside 5'-monophosphate N-glycosidase activity / deoxyribonucleoside monophosphate catabolic process / 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 5'-monophosphate N-glycosidase activity / deoxyribonucleoside monophosphate catabolic process / 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
N6-ISOPENTENYL-ADENOSINE-5'-MONOPHOSPHATE / 5-hydroxymethyl-dUMP N-hydrolase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.24 Å
AuthorsPadilla, A. / Labesse, G. / Kaminski, P.A.
Citation
Journal: Plos One / Year: 2013
Title: N (6)-substituted AMPs inhibit mammalian deoxynucleotide N-hydrolase DNPH1.
Authors: Amiable, C. / Pochet, S. / Padilla, A. / Labesse, G. / Kaminski, P.A.
#1: Journal: Acta Crystallogr.,Sect.D / 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
DepositionMay 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 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 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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


Theoretical massNumber of molelcules
Total (without water)70,3638
Polymers68,6934
Non-polymers1,6694
Water3,297183
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)35,1814
Polymers34,3472
Non-polymers8352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-42 kcal/mol
Surface area10590 Å2
MethodPISA
2
C: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1
D: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1814
Polymers34,3472
Non-polymers8352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-42 kcal/mol
Surface area10710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.146, 96.568, 79.034
Angle α, β, γ (deg.)90.000, 101.580, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22C

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: 6IA / End label comp-ID: 6IA / Refine code: 6 / Auth seq-ID: 10 - 201 / Label seq-ID: 3

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA - E
21DD - H
12BB - F
22CC - G

NCS ensembles :
ID
1
2

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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.: 4 / Fragment: UNP residues 11-151 / Mutation: D69N
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-6IA / N6-ISOPENTENYL-ADENOSINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 417.354 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H24N5O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG8K, 100 MM NaCaCo, 200 MM ZINC ACETATE, PH 6.5, vapor diffusion, hanging drop, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979756 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 18, 2010
RadiationMonochromator: CHANNEL CUT ESRF MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979756 Å / Relative weight: 1
ReflectionResolution: 2.24→40.97 Å / Num. obs: 21068 / % possible obs: 92.04 % / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.1
Reflection shellResolution: 2.24→2.39 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.107 / Mean I/σ(I) obs: 6.7 / % possible all: 65.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FYI

4fyi


Resolution: 2.24→38.71 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.895 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 14.052 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.596 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 1077 5.1 %RANDOM
Rwork0.1738 ---
obs0.1765 20988 92.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 44.69 Å2 / Biso mean: 15.7391 Å2 / Biso min: 4.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20.1 Å2
2--0.14 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.24→38.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4139 0 112 183 4434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224358
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.9825897
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1965517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41722.455220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1215697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8961551
X-RAY DIFFRACTIONr_chiral_restr0.0770.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023347
X-RAY DIFFRACTIONr_mcbond_it0.3151.52579
X-RAY DIFFRACTIONr_mcangle_it0.60324099
X-RAY DIFFRACTIONr_scbond_it0.99931779
X-RAY DIFFRACTIONr_scangle_it1.5944.51798
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1030LOOSE POSITIONAL0.355
1A1030LOOSE THERMAL0.8910
2B1056LOOSE POSITIONAL0.35
2B1056LOOSE THERMAL0.9910
LS refinement shellResolution: 2.24→2.298 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 56 -
Rwork0.178 948 -
all-1004 -
obs--58.44 %
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)
11.2835-0.29930.07252.00390.41862.4380.04350.1497-0.1559-0.1462-0.0312-0.04970.22130.0219-0.01230.03960.00360.00780.0311-0.01610.04679.09610.027729.4351
21.8151-0.091-0.05011.33070.19431.26550.025-0.01350.2193-0.0152-0.0150.0295-0.1763-0.0581-0.010.02530.00890.00580.0147-0.00510.04143.037318.370743.2528
32.47970.11280.47641.85280.30161.37160.0178-0.0579-0.2755-0.0090.0282-0.02480.2542-0.0757-0.0460.0527-0.01570.00650.0356-0.00530.06993.1014-9.236465.5462
41.69660.4907-0.09681.44350.01542.47320.0613-0.19670.20120.1586-0.0603-0.0304-0.25210.0088-0.0010.05220.00060.01060.0565-0.02230.05889.27049.444778.9971
50.1725-0.0114-0.01970.186-0.26770.92560.01520.0107-0.0117-0.040.00240.0081-0.00410.0014-0.01750.04740.00480.01390.0961-0.00880.14783.39455.831249.8899
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 151
2X-RAY DIFFRACTION1A201
3X-RAY DIFFRACTION2B10 - 152
4X-RAY DIFFRACTION2B201
5X-RAY DIFFRACTION3C10 - 152
6X-RAY DIFFRACTION3C201
7X-RAY DIFFRACTION4D10 - 152
8X-RAY DIFFRACTION4D201
9X-RAY DIFFRACTION5A301 - 373
10X-RAY DIFFRACTION5A374 - 443
11X-RAY DIFFRACTION5B301 - 317
12X-RAY DIFFRACTION5C301 - 309
13X-RAY DIFFRACTION5D301 - 314

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