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- PDB-4kxl: Crystal structure of DNPH1 (RCL) with 6-CYCLOPENTYL-AMP -

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Basic information

Entry
Database: PDB / ID: 4kxl
TitleCrystal structure of DNPH1 (RCL) with 6-CYCLOPENTYL-AMP
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
N-cyclopentyladenosine 5'-(dihydrogen phosphate) / 5-hydroxymethyl-dUMP N-hydrolase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.69 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)70,54710
Polymers68,6934
Non-polymers1,8536
Water8,953497
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)35,1774
Polymers34,3472
Non-polymers8312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-27 kcal/mol
Surface area11050 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)35,3696
Polymers34,3472
Non-polymers1,0234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-41 kcal/mol
Surface area11500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.728, 100.644, 79.681
Angle α, β, γ (deg.)90.00, 101.79, 90.00
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-6C6 / N-cyclopentyladenosine 5'-(dihydrogen phosphate)


Mass: 415.338 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N5O7P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / 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

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.23 %
Crystal growTemperature: 291 K / Method: hanging drop / pH: 7.6
Details: 100 MM TRIS, 1.1 AMMONIUM SULPHATE, 20MM MGSO4, PH 7.6, hanging drop, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 25, 2010
RadiationMonochromator: CHANNEL CUT ESRF MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.69→32.03 Å / Num. obs: 53250 / % possible obs: 93.88 % / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 5.4
Reflection shellResolution: 1.69→1.79 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.115 / Mean I/σ(I) obs: 2.6 / % possible all: 75.8

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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: 1.69→27.02 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 4.665 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2125 2671 5 %RANDOM
Rwork0.176 ---
obs0.1778 52987 93.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 59.06 Å2 / Biso mean: 16.691 Å2 / Biso min: 4.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.05 Å2
2--0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.69→27.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4195 0 122 497 4814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224472
X-RAY DIFFRACTIONr_bond_other_d0.0020.023112
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.9876050
X-RAY DIFFRACTIONr_angle_other_deg0.8153.0037344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1835523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.10222.13230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51215734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3851559
X-RAY DIFFRACTIONr_chiral_restr0.1110.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024950
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021017
X-RAY DIFFRACTIONr_mcbond_it0.4771.52617
X-RAY DIFFRACTIONr_mcbond_other0.1331.51101
X-RAY DIFFRACTIONr_mcangle_it0.84824172
X-RAY DIFFRACTIONr_scbond_it1.43931855
X-RAY DIFFRACTIONr_scangle_it2.2064.51878
LS refinement shellResolution: 1.69→1.734 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 155 -
Rwork0.223 2807 -
all-2962 -
obs--70.36 %
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)
11.14960.2172-0.04161.17310.44242.7455-0.0221-0.10250.13590.1046-0.0190.0093-0.1820.06270.04120.0404-0.0105-0.00190.057-0.01680.0499.3589.86976.85
21.1601-0.19580.44522.14730.47151.8374-0.0117-0.0413-0.24140.1351-0.07630.170.3655-0.22060.0880.0933-0.05540.04490.0762-0.02650.09313.355-8.87963.203
31.2237-0.1344-0.61451.6870.32461.59470.02060.00950.218-0.0341-0.04780.0791-0.3098-0.10970.02720.07910.0361-0.03740.0459-0.02310.073.28818.97640.536
41.3994-0.2819-0.02451.26020.25752.4559-0.02390.0708-0.1686-0.1142-0.0214-0.00240.20880.00640.04520.04990.0095-0.00780.0175-0.01460.04959.273-0.34827.248
50.3045-0.00490.04370.2312-0.0641.9051-0.0196-0.00370.0040.009-0.03480.0058-0.01520.02270.05440.13060.0015-0.00640.1575-0.02210.21365.7095.86751.076
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 152
2X-RAY DIFFRACTION1A201
3X-RAY DIFFRACTION2B10 - 151
4X-RAY DIFFRACTION2B201
5X-RAY DIFFRACTION3C9 - 152
6X-RAY DIFFRACTION3C201
7X-RAY DIFFRACTION4D9 - 152
8X-RAY DIFFRACTION4D201
9X-RAY DIFFRACTION5C202
10X-RAY DIFFRACTION5D202
11X-RAY DIFFRACTION5A301 - 432
12X-RAY DIFFRACTION5B301 - 406
13X-RAY DIFFRACTION5C301 - 423
14X-RAY DIFFRACTION5D301 - 436

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