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- PDB-4fyi: Crystal structure of rcl with 6-cyclopentyl-AMP -

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Basic information

Entry
Database: PDB / ID: 4fyi
TitleCrystal structure of rcl with 6-cyclopentyl-AMP
ComponentsDeoxyribonucleoside 5'-monophosphate N-glycosidase
KeywordsHYDROLASE / Deoxyribonucleoside 5'-monophosphate N-glycosidase
Function / homology
Function and homology information


deoxyribonucleoside 5'-monophosphate N-glycosidase activity / deoxyribonucleoside monophosphate catabolic process / Purine catabolism / 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 ...deoxyribonucleoside 5'-monophosphate N-glycosidase activity / deoxyribonucleoside monophosphate catabolic process / Purine catabolism / 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 / Resolution: 1.96 Å
AuthorsLabesse, G. / Padilla, A. / Kaminski, P.A.
CitationJournal: 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
DepositionJul 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Deoxyribonucleoside 5'-monophosphate N-glycosidase
B: Deoxyribonucleoside 5'-monophosphate N-glycosidase
C: Deoxyribonucleoside 5'-monophosphate N-glycosidase
D: Deoxyribonucleoside 5'-monophosphate N-glycosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3558
Polymers68,6934
Non-polymers1,6614
Water7,278404
1
A: Deoxyribonucleoside 5'-monophosphate N-glycosidase
B: Deoxyribonucleoside 5'-monophosphate N-glycosidase
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-28 kcal/mol
Surface area11000 Å2
MethodPISA
2
C: Deoxyribonucleoside 5'-monophosphate N-glycosidase
D: Deoxyribonucleoside 5'-monophosphate N-glycosidase
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-29 kcal/mol
Surface area10730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.567, 118.873, 57.537
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
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: Rcl / Production host: Escherichia coli (E. coli)
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.28 Å3/Da / Density % sol: 46.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 100 mM Tris, 1.1 Ammonium Sulphate, 20 mM MgAcetate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 291.K

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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: Apr 22, 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: 1.96→42.5 Å / Num. all: 50458 / Num. obs: 48894 / % possible obs: 96.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.7 %
Reflection shellResolution: 1.96→2 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.364 / % possible all: 92.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→42.5 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.073 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2240 5 %RANDOM
Rwork0.17899 ---
obs0.18082 42198 96.9 %-
all-50458 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.806 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20 Å20 Å2
2---0.26 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.96→42.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3974 0 112 404 4490
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224239
X-RAY DIFFRACTIONr_bond_other_d0.0030.022970
X-RAY DIFFRACTIONr_angle_refined_deg1.161.9845732
X-RAY DIFFRACTIONr_angle_other_deg0.8133.0036989
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1555505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.59521.982217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45415687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0921558
X-RAY DIFFRACTIONr_chiral_restr0.0720.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024733
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02977
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5351.52499
X-RAY DIFFRACTIONr_mcbond_other0.1061.51057
X-RAY DIFFRACTIONr_mcangle_it1.00923966
X-RAY DIFFRACTIONr_scbond_it1.27131740
X-RAY DIFFRACTIONr_scangle_it2.0284.51762
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 163 -
Rwork0.239 2966 -
obs--93.82 %
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)
11.47710.17380.18150.41010.15881.53930.12950.08740.1203-0.063-0.13670.02250.1096-0.0030.00710.07760.0457-0.01850.06070.00010.028642.63515.90315.9596
20.5268-0.3182-0.26340.4490.06420.747-0.0525-0.0315-0.00740.06030.01290.02260.03240.00450.03960.07690.01010.00350.0254-0.01330.056439.395615.210329.3443
30.41990.10490.14630.69410.24790.82020.00290.0257-0.0219-0.0666-0.01150.0159-0.04280.02860.00860.05260.00270.02750.0413-0.00550.053530.792745.761834.4317
41.37010.0258-0.460.12590.32151.4534-0.0818-0.2862-0.0663-0.01320.02640.03430.03950.16560.05530.04120.02060.01490.10510.02670.035333.954746.830557.6128
50.0832-0.1637-0.15650.33980.2870.33460.0096-0.0028-0.0065-0.01120.00010.03290.00650.0149-0.00970.05970.00590.01490.0419-0.0110.065135.592431.956131.3945
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 150
2X-RAY DIFFRACTION1A201
3X-RAY DIFFRACTION2B10 - 150
4X-RAY DIFFRACTION2B201
5X-RAY DIFFRACTION3C10 - 149
6X-RAY DIFFRACTION3C201
7X-RAY DIFFRACTION4D10 - 149
8X-RAY DIFFRACTION4D201
9X-RAY DIFFRACTION5A301 - 378
10X-RAY DIFFRACTION5B301 - 418
11X-RAY DIFFRACTION5C301 - 423
12X-RAY DIFFRACTION5D301 - 385

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