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- PDB-2g08: X-ray structure of mouse pyrimidine 5'-nucleotidase type 1, produ... -

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Basic information

Entry
Database: PDB / ID: 2g08
TitleX-ray structure of mouse pyrimidine 5'-nucleotidase type 1, product-transition complex analog with Aluminum fluoride
ComponentsCytosolic 5'-nucleotidase III
KeywordsHYDROLASE / UniProt Q9D020 / UMPH-1 / Cytosolic 5'-nucleotidase III / Pyrimidine 5'-nucleotidase 1 / P5n-1 / NT5C3 PROTEIN / AAH38029 / BC038029 / MM.158936 / Lead Poisoning / STRUCTURAL GENOMICS FUNCTIONAL FOLLOW-UP STUDY / PROTEIN STRUCTURE INITIATIVE / PSI / CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS / CESG
Function / homology
Function and homology information


Pyrimidine catabolism / CMP catabolic process / dTMP catabolic process / UMP catabolic process / dCMP catabolic process / dUMP catabolic process / 7-methylguanosine nucleotidase / adenosine metabolic process / XMP 5'-nucleosidase activity / 5'-nucleotidase ...Pyrimidine catabolism / CMP catabolic process / dTMP catabolic process / UMP catabolic process / dCMP catabolic process / dUMP catabolic process / 7-methylguanosine nucleotidase / adenosine metabolic process / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / transferase activity / defense response to virus / nuclear body / nucleotide binding / magnesium ion binding / endoplasmic reticulum / mitochondrion / nucleoplasm / 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
ALUMINUM FLUORIDE / Cytosolic 5'-nucleotidase 3A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBitto, E. / Bingman, C.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structure of pyrimidine 5'-nucleotidase type 1. Insight into mechanism of action and inhibition during lead poisoning.
Authors: Bitto, E. / Bingman, C.A. / Wesenberg, G.E. / McCoy, J.G. / Phillips, G.N.
History
DepositionFeb 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 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_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_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytosolic 5'-nucleotidase III
B: Cytosolic 5'-nucleotidase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5446
Polymers68,3282
Non-polymers2174
Water8,629479
1
A: Cytosolic 5'-nucleotidase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2723
Polymers34,1641
Non-polymers1082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytosolic 5'-nucleotidase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2723
Polymers34,1641
Non-polymers1082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.044, 135.044, 39.049
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 2 / Auth seq-ID: 7 - 297 / Label seq-ID: 7 - 297

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological unit is a monomer. There are 2 biological units in the asymmetric unit (chains A & B).

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Components

#1: Protein Cytosolic 5'-nucleotidase III / cN-III / Pyrimidine 5'- nucleotidase 1 / P5'N-1 / P5N-1 / PN-I / Lupin


Mass: 34163.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: NT5C3 / Plasmid: PVP 16 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q9D020, lysophospholipase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


Mass: 83.977 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 3.01 Å3/Da / Density % sol: 59.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.005 M BIS TRIS, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, PH 6.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (20-25% PEG 8K, 0.10 M ...Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.005 M BIS TRIS, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, PH 6.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (20-25% PEG 8K, 0.10 M PIPES PH 6.5) CRYSTALS SOAKED FOR 20 MINUTES IN WELL SOLUTION WITH 0.060 M magnesium chloride, 0.003 M aluminum chloride, 0.050 M sodium fluoride, 0.010 M uridine, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER PROTEUM-R / Detector: CCD / Date: Dec 18, 2005 / Details: MONTEL OPTICS
RadiationMonochromator: Graded Multilayer / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→67.52 Å / Num. obs: 33163 / % possible obs: 99.9 % / Redundancy: 16.69 % / Rmerge(I) obs: 0.0991 / Net I/σ(I): 19.01
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.35-2.46.080.73631.9420391100
2.4-2.456.790.61792.5618711100
2.45-2.57.180.60362.7516831100
2.5-2.67.910.49783.3931321100
2.6-2.79.20.39674.4425681100
2.7-2.810.690.30346.1622741100
2.8-2.911.690.24367.8719541100
2.9-3.05130.213610.0924751100
3.05-3.214.380.199513.2520471100
3.2-3.416.380.157518.9521451100
3.4-3.6521.460.134426.7321481100
3.65-3.9526.380.10535.081854199.9
3.95-4.3528.510.077943.117681100
4.35-5310.070849.2617841100
5-6.334.620.075148.5517111100
6.3-67.5237.20.061760.421710198.7

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
SAINTdata reduction
SADABSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2BDU

2bdu


Resolution: 2.35→67.52 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.176 / SU B: 14.714 / SU ML: 0.19 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.252 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2603 1673 5.065 %RANDOM
Rwork0.1901 ---
all0.194 ---
obs0.194 33031 99.563 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 43.413 Å2
Baniso -1Baniso -2Baniso -3
1-0.858 Å20.429 Å20 Å2
2--0.858 Å20 Å2
3----1.287 Å2
Refinement stepCycle: LAST / Resolution: 2.35→67.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4652 0 10 479 5141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224748
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.9726380
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4675580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.89325.405222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.83615904
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1241518
X-RAY DIFFRACTIONr_chiral_restr0.1040.2718
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023500
X-RAY DIFFRACTIONr_nbd_refined0.2050.22361
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23191
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2398
X-RAY DIFFRACTIONr_metal_ion_refined0.0560.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.26
X-RAY DIFFRACTIONr_mcbond_it0.7011.52996
X-RAY DIFFRACTIONr_mcangle_it1.12224670
X-RAY DIFFRACTIONr_scbond_it1.92331977
X-RAY DIFFRACTIONr_scangle_it2.8754.51710
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1164TIGHT POSITIONAL0.020.05
1162MEDIUM POSITIONAL0.2680.5
1164TIGHT THERMAL0.0760.5
1162MEDIUM THERMAL0.3422
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
2.35-2.4110.3571240.27323260.277245399.878
2.411-2.4770.3441260.24722700.2512396100
2.477-2.5490.3181160.24622280.249234599.957
2.549-2.6270.2921140.26521250.266224199.911
2.627-2.7130.3481120.23520570.24217299.862
2.713-2.8090.3061060.23520540.239216699.723
2.809-2.9150.3561050.22718750.233198899.598
2.915-3.0340.336810.20919030.213199599.449
3.034-3.1680.312990.19917500.204186399.249
3.168-3.3230.228950.18917180.191181799.78
3.323-3.5020.277890.17516430.18173799.712
3.502-3.7150.232670.16915290.171160199.688
3.715-3.9710.185740.15914460.16152999.411
3.971-4.2890.24710.1413330.145141699.153
4.289-4.6970.207750.14212260.145131598.935
4.697-5.2510.201640.16210860.164116099.138
5.251-6.0610.272540.1979780.201103699.614
6.061-7.4180.275470.1978490.20189999.666
7.418-10.470.186340.1476360.14967399.554
10.47-117.0410.24200.2363260.23637492.513
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)
14.2269-0.4624-1.24052.89410.25713.00910.22080.14720.3388-0.0965-0.0790.1259-0.2634-0.1195-0.1419-0.1282-0.00910.0312-0.19490.0688-0.251237.85476.47727.545
24.1378-0.64291.16782.9062-0.30182.94410.22230.1367-0.349-0.0833-0.0871-0.1250.28510.1226-0.1352-0.135-0.005-0.0304-0.1924-0.0717-0.246129.64640.47927.542
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 7 - 297 / Label seq-ID: 7 - 297

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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