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- PDB-4kxn: Crystal structure of DNPH1 (RCL) with kinetine riboside monophosphate -

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Basic information

Entry
Database: PDB / ID: 4kxn
TitleCrystal structure of DNPH1 (RCL) with kinetine riboside monophosphate
Components2'-deoxynucleoside 5'-phosphate N-hydrolase 1
KeywordsHYDROLASE / DEOXYRIBONUCLEOSIDE 5'-MONOPHOSPHATE N-GLYCOSIDASE
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-6K6 / 5-hydroxymethyl-dUMP N-hydrolase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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_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_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

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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)70,4038
Polymers68,6934
Non-polymers1,7094
Water4,378243
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)35,2014
Polymers34,3472
Non-polymers8552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-26 kcal/mol
Surface area10640 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)35,2014
Polymers34,3472
Non-polymers8552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-27 kcal/mol
Surface area10780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.238, 95.449, 79.288
Angle α, β, γ (deg.)90.000, 101.560, 90.000
Int Tables number4
Space group name H-MP1211

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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-6K6 / N-(furan-2-ylmethyl)adenosine 5'-(dihydrogen phosphate)


Mass: 427.306 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H18N5O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 7.6
Details: 100 MM TRIS, 1.2 M AMMONIUM SULPHATE, 20MM MGCL2, PH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 18, 2011
RadiationMonochromator: CHANNEL CUT ESRF MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.9→29.97 Å / Num. obs: 36476 / % possible obs: 98.6 % / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 2.1 / % possible all: 96.6

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4fyi


Resolution: 1.9→23.86 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.83 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 12.292 / SU ML: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1818 5 %RANDOM
Rwork0.2322 ---
obs0.2348 36376 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 52.42 Å2 / Biso mean: 17.2637 Å2 / Biso min: 3.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20.09 Å2
2--0.23 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.9→23.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4043 0 116 243 4402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224262
X-RAY DIFFRACTIONr_angle_refined_deg1.8961.9865764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3815505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29422.243214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.92715679
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0321552
X-RAY DIFFRACTIONr_chiral_restr0.1860.2613
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023276
X-RAY DIFFRACTIONr_mcbond_it0.3771.52516
X-RAY DIFFRACTIONr_mcangle_it0.6723991
X-RAY DIFFRACTIONr_scbond_it1.12931746
X-RAY DIFFRACTIONr_scangle_it1.6764.51773
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 125 -
Rwork0.3 2432 -
all-2557 -
obs--96.16 %
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)
11.5892-0.04560.25091.3805-0.15282.64740.01430.1851-0.2057-0.22450.0091-0.07760.24740.0572-0.02340.06610.00900.0271-0.03110.05359.156-0.09129.511
21.68610.0125-0.27831.47580.13470.7913-0.0232-0.06080.21210.0480.02530.0269-0.1496-0.0055-0.00210.03670.0071-0.01190.0059-0.01390.04113.39618.00843.48
31.3606-0.10810.17871.1859-0.00211.31940.0112-0.0305-0.2335-0.0004-0.01660.01070.1981-0.02390.00530.0411-0.01410.00370.0215-0.00920.06263.481-9.08965.211
41.56190.13270.15651.0346-0.21371.77950.0083-0.24130.24740.15880.01750.0008-0.22970.0203-0.02580.0651-0.0023-0.00470.0731-0.04140.0649.2659.39678.679
50.3086-0.0290.07480.2959-0.10870.9563-0.0008-0.02380.01150.0150.0093-0.0408-0.00320.0157-0.00860.0710.00320.01320.0995-0.02260.12853.875.93652.684
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 150
2X-RAY DIFFRACTION1A201
3X-RAY DIFFRACTION2B10 - 152
4X-RAY DIFFRACTION2B201
5X-RAY DIFFRACTION3C10 - 151
6X-RAY DIFFRACTION3C201
7X-RAY DIFFRACTION4D10 - 150
8X-RAY DIFFRACTION4D201
9X-RAY DIFFRACTION5A301 - 369
10X-RAY DIFFRACTION5B301 - 367
11X-RAY DIFFRACTION5C301 - 354
12X-RAY DIFFRACTION5D301 - 353

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