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- PDB-2g06: X-ray structure of mouse pyrimidine 5'-nucleotidase type 1, with ... -

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Basic information

Entry
Database: PDB / ID: 2g06
TitleX-ray structure of mouse pyrimidine 5'-nucleotidase type 1, with bound magnesium(II)
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 / dCMP catabolic process / UMP catabolic process / dUMP catabolic process / 7-methylguanosine nucleotidase / adenosine metabolic process / 5'-nucleotidase / 5'-nucleotidase activity ...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 / cytoplasm / cytosol
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
Cytosolic 5'-nucleotidase 3A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 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_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 / _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_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_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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)68,9816
Polymers68,3282
Non-polymers6534
Water14,682815
1
A: Cytosolic 5'-nucleotidase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4913
Polymers34,1641
Non-polymers3272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytosolic 5'-nucleotidase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4913
Polymers34,1641
Non-polymers3272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.343, 134.343, 39.152
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, 5'-nucleotidase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PIN / PIPERAZINE-N,N'-BIS(2-ETHANESULFONIC ACID) / PIPES / 1,4-PIPERAZINEDIETHANESULFONIC ACID


Mass: 302.368 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O6S2 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 815 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.98 Å3/Da / Density % sol: 58.79 %
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 15 MINUTES IN WELL SOLUTION WITH 0.005 M magnesium chloride, temperature 277K, VAPOR DIFFUSION, HANGING DROP

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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: Jan 3, 2006 / Details: MONTEL OPTICS
RadiationMonochromator: Graded Multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→67.17 Å / Num. obs: 37523 / % possible obs: 100 % / Redundancy: 17.82 % / Rmerge(I) obs: 0.1006 / Net I/σ(I): 20.61
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.25-2.36.470.63712.6724231100
2.3-2.358.110.60443.3321871100
2.35-2.49.310.51964.1820161100
2.4-2.511.420.47265.235481100
2.5-2.612.730.39226.4330571100
2.6-2.713.590.31687.9525691100
2.7-2.814.820.27199.9422941100
2.8-2.9515.760.238312.5127771100
2.95-3.115.770.200615.1622861100
3.1-3.315.990.161719.4524951100
3.3-3.518.420.125527.231918199.6
3.5-3.821.150.09934.4721681100
3.8-4.226.640.078243.8520061100
4.2-4.831.30.067453.319261100
4.8-6.137.080.070554.2119711100
6.1-67.1742.70.058767.691882199.8

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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: 2.25→67.17 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.147 / SU B: 10.501 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.198 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2193 1899 5.063 %RANDOM
Rwork0.1548 ---
all0.158 ---
obs0.158 37505 99.955 %-
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: 35.072 Å2
Baniso -1Baniso -2Baniso -3
1-0.204 Å20.102 Å20 Å2
2--0.204 Å20 Å2
3----0.307 Å2
Refinement stepCycle: LAST / Resolution: 2.25→67.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4652 0 38 815 5505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224789
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9796449
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8935584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.77425.426223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.51615908
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5551518
X-RAY DIFFRACTIONr_chiral_restr0.1070.2728
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023516
X-RAY DIFFRACTIONr_nbd_refined0.2070.22463
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23218
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2633
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2490.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.214
X-RAY DIFFRACTIONr_mcbond_it1.29122987
X-RAY DIFFRACTIONr_mcangle_it2.23644687
X-RAY DIFFRACTIONr_scbond_it4.38962014
X-RAY DIFFRACTIONr_scangle_it5.96981761
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
1159TIGHT POSITIONAL0.0260.05
1158MEDIUM POSITIONAL0.2210.5
1159TIGHT THERMAL0.1190.5
1158MEDIUM THERMAL0.7892
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 (%)
2.25-2.3090.3141510.21926730.224282799.894
2.309-2.3720.2991320.225540.2052686100
2.372-2.4410.2891260.19525150.1992641100
2.441-2.5160.2391350.18823930.1912528100
2.516-2.5980.2461310.18423660.1872497100
2.598-2.6890.2711220.18422570.1882379100
2.689-2.7910.2991100.17122300.1772340100
2.791-2.9050.2431170.15920410.1632158100
2.905-3.0340.248900.16121010.1642191100
3.034-3.1820.211110.1519200.1542031100
3.182-3.3540.183970.14618010.148190299.79
3.354-3.5570.223840.13617760.139186499.785
3.557-3.8020.174850.12716260.1291711100
3.802-4.1070.185720.1215170.1231589100
4.107-4.4980.183840.1213900.1241474100
4.498-5.0280.188770.12812700.1311347100
5.028-5.8040.195600.16211130.1641173100
5.804-7.1040.226560.179390.173995100
7.104-10.0280.161370.1477330.148770100
10.028-116.2480.192220.183910.18141998.568
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)
13.7270.1648-0.6732.340.26491.1280.07370.04580.1491-0.1397-0.03150.0498-0.04840.0437-0.0422-0.0926-0.00010.014-0.12720.0352-0.193239.99573.45826.305
23.68980.1530.77632.4225-0.23211.15670.08860.0229-0.1551-0.1343-0.0441-0.05710.0911-0.0252-0.0445-0.098-0.006-0.0173-0.1267-0.0378-0.191127.242.87526.303
35.27861.19890.41372.84850.81591.8530.1976-0.24540.7780.14260.00940.6085-0.2877-0.06-0.2070.06680.06030.0952-0.0821-0.02060.099926.37689.38634.077
46.541.4222-0.75713.2942-0.67121.71950.3076-0.2767-0.72310.1297-0.0863-0.59150.19680.095-0.22130.07070.0319-0.1097-0.10130.04420.081640.76926.94434.066
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA7 - 777 - 77
21AA125 - 295125 - 295
32BB7 - 777 - 77
42BB125 - 295125 - 295
53AA78 - 12478 - 124
64BB78 - 12478 - 124

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