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Basic information

Entry
Database: PDB / ID: 4kx3
TitleStructure of murine cytosolic 5'-nucleotidase III complexed with thymidine monophosphate
ComponentsIsoform 1 of Cytosolic 5'-nucleotidase 3A
KeywordsHYDROLASE / SUBSTRATE COMPLEX / HAD SUPERFAMILY / NUCLEOTIDASE / UMPH-1 / CYTOSOLIC 5'-NUCLEOTIDASE III / P5N-1
Function / homology
Function and homology information


Pyrimidine catabolism / CMP catabolic process / dTMP catabolic process / dCMP catabolic process / UMP catabolic process / dUMP catabolic process / 7-methylguanosine nucleotidase / adenosine metabolic process / : / 5'-nucleotidase ...Pyrimidine catabolism / CMP catabolic process / dTMP catabolic process / dCMP catabolic process / UMP catabolic process / dUMP catabolic process / 7-methylguanosine nucleotidase / adenosine metabolic process / : / 5'-nucleotidase / 5'-nucleotidase activity / transferase activity / nuclear body / nucleotide binding / magnesium ion binding / endoplasmic reticulum / mitochondrion / cytosol / cytoplasm
Similarity search - Function
Pyrimidine 5'-nucleotidase (UMPH-1), N-terminal domain / Pyrimidine 5'-nucleotidase, eukaryotic / Pyrimidine 5'-nucleotidase (UMPH-1) / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Pyrimidine 5'-nucleotidase (UMPH-1), N-terminal domain / Pyrimidine 5'-nucleotidase, eukaryotic / Pyrimidine 5'-nucleotidase (UMPH-1) / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
THYMIDINE-5'-PHOSPHATE / Cytosolic 5'-nucleotidase 3A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsBitto, E. / Bingman, C.A. / Grobosky, C.L.
CitationJournal: To be Published
Title: Structure of murine cytosolic 5'-nucleotidase III complexed with thymidine monophosphate
Authors: Bitto, E. / Bingman, C.A. / Grobosky, C.L.
History
DepositionMay 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Feb 12, 2025Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_ref / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity_name_com.name / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_entry_details.has_protein_modification / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_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.ptnr3_auth_comp_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_special_symmetry.label_asym_id / _struct_ref.db_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 1 of Cytosolic 5'-nucleotidase 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7738
Polymers33,9401
Non-polymers8337
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.872, 46.872, 285.873
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-425-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Isoform 1 of Cytosolic 5'-nucleotidase 3A / 7-methylguanosine phosphate-specific 5'-nucleotidase / 7-methylguanosine nucleotidase / Cytosolic ...7-methylguanosine phosphate-specific 5'-nucleotidase / 7-methylguanosine nucleotidase / Cytosolic 5'-nucleotidase 3 / Cytosolic 5'-nucleotidase III / cN-III / Lupin / Pyrimidine 5'-nucleotidase 1 / P5'N-1 / P5N-1 / PN-I


Mass: 33940.020 Da / Num. of mol.: 1 / Fragment: Catalytically Inactive cN-III / Mutation: D51N, M1S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nt5c3a, Nt5c3 / Plasmid: pVP16-GW / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2
References: UniProt: Q9D020, 5'-nucleotidase, 7-methylguanosine nucleotidase

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Non-polymers , 5 types, 253 molecules

#2: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE CRYSTALLIZED SEQUENCE REFERS TO Q9D020-1|5NT3_MOUSE ISOFORM 1 OF CYTOSOLIC 5'-NUCLEOTIDASE

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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: 2.32 Å3/Da / Density % sol: 46.99 %
Crystal growTemperature: 283 K / Method: vapor diffusion / pH: 8
Details: 20% PEG 3350, 0.10 M HEPES, 0.050 M Ammonium Acetate, VAPOR DIFFUSION, temperature 283K, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 23, 2013 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 19954 / Num. obs: 19922 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 13.8 % / Biso Wilson estimate: 20.425 Å2 / Rmerge(I) obs: 0.118 / Rsym value: 0.086 / Χ2: 1.156 / Net I/σ(I): 6.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.1414.30.5869980.8011100
2.14-2.1814.30.5139300.8371100
2.18-2.2214.20.479820.8411100
2.22-2.2614.10.4239401.0771100
2.26-2.3114.30.3859640.9111100
2.31-2.3714.20.3189890.9591100
2.37-2.4214.30.2929480.9661100
2.42-2.4914.20.2769810.9561100
2.49-2.5614.20.249771.0111100
2.56-2.6514.20.219781.0341100
2.65-2.7414.10.1849871.0981100
2.74-2.8514.10.1579641.1771100
2.85-2.98140.14310011.1861100
2.98-3.14140.12110061.4021100
3.14-3.3313.90.1019921.445199.8
3.33-3.5913.80.08810021.5811100
3.59-3.9513.50.07210131.573199.9
3.95-4.5213.40.05810281.3731100
4.52-5.7130.05410701.3451100
5.7-5011.50.04811721.575198.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FE3

4fe3


Resolution: 2.1→46.92 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2034 / WRfactor Rwork: 0.1441 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8807 / SU B: 3.885 / SU ML: 0.104 / SU R Cruickshank DPI: 0.1849 / SU Rfree: 0.1733 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2165 991 5 %RANDOM
Rwork0.1531 ---
obs0.1561 19848 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.3 Å2 / Biso mean: 28.3699 Å2 / Biso min: 11.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2--0.32 Å2-0 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2326 0 61 246 2633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192439
X-RAY DIFFRACTIONr_bond_other_d0.0010.022387
X-RAY DIFFRACTIONr_angle_refined_deg1.7591.9743274
X-RAY DIFFRACTIONr_angle_other_deg0.84535510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9385294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.08125.405111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33615454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.827159
X-RAY DIFFRACTIONr_chiral_restr0.1040.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022699
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02526
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 80 -
Rwork0.173 1341 -
all-1421 -
obs--99.93 %

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