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- PDB-2g07: X-ray structure of mouse pyrimidine 5'-nucleotidase type 1, phosp... -

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Basic information

Entry
Database: PDB / ID: 2g07
TitleX-ray structure of mouse pyrimidine 5'-nucleotidase type 1, phospho-enzyme intermediate analog with Beryllium 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 / 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: 2.3 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 / _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 13, 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)68,5064
Polymers68,4582
Non-polymers492
Water9,692538
1
A: Cytosolic 5'-nucleotidase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2532
Polymers34,2291
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytosolic 5'-nucleotidase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2532
Polymers34,2291
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.834, 134.834, 38.945
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: 34228.926 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / 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 20 MINUTES IN WELL SOLUTION WITH 0.060 M magnesium chloride, 0.003 M beryllium fluoride, 0.050 M sodium fluoride, 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: Jan 20, 2006 / Details: MONTEL OPTICS
RadiationMonochromator: Graded Multilayer / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→67.42 Å / Num. obs: 33047 / % possible obs: 93.9 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.1278 / Net I/σ(I): 11.32
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.3-2.354.110.63561.991805183.8
2.35-2.454.710.54672.63332185
2.45-2.555.730.48183.42860186.3
2.55-2.656.240.43273.962444187.8
2.65-2.756.680.34215.282215191.2
2.75-2.857.240.30636.021923194.3
2.85-2.957.630.26957.071826197.4
2.95-3.17.920.24918.142250199
3.1-3.258.150.200310.41925199.9
3.25-3.458.240.152713.4320361100
3.45-3.78.280.122416.381998199.9
3.7-48.610.099419.3217571100
4-4.49.090.087421.716591100
4.4-5.0510.470.084324.5316801100
5.05-6.3513.350.093625.7316651100
6.35-67.4214.840.075832.231672199.8

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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: 2.3→67.42 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.259 / WRfactor Rwork: 0.18 / SU B: 13.722 / SU ML: 0.183 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.302 / ESU R Free: 0.252 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2585 1673 5.066 %RANDOM
Rwork0.1799 ---
all0.184 ---
obs0.184 33027 93.901 %-
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: 38.491 Å2
Baniso -1Baniso -2Baniso -3
1--0.155 Å2-0.078 Å20 Å2
2---0.155 Å20 Å2
3---0.233 Å2
Refinement stepCycle: LAST / Resolution: 2.3→67.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4660 0 2 538 5200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224749
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.9756388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5045580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.60825.364220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.42315902
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7731518
X-RAY DIFFRACTIONr_chiral_restr0.1190.2720
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023500
X-RAY DIFFRACTIONr_nbd_refined0.2090.22272
X-RAY DIFFRACTIONr_nbtor_refined0.3050.23163
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2408
X-RAY DIFFRACTIONr_metal_ion_refined0.0510.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.214
X-RAY DIFFRACTIONr_mcbond_it0.841.52983
X-RAY DIFFRACTIONr_mcangle_it1.21924670
X-RAY DIFFRACTIONr_scbond_it2.12731980
X-RAY DIFFRACTIONr_scangle_it3.0634.51718
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 POSITIONAL0.0360.05
1166MEDIUM POSITIONAL0.2960.5
1164TIGHT THERMAL0.1830.5
1166MEDIUM THERMAL0.6572
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 (%)
2.3-2.360.311080.23820700.242259683.898
2.36-2.4240.3631100.2420510.246254884.812
2.424-2.4950.3551070.2219820.226243085.967
2.495-2.5710.2991070.22620060.23242087.314
2.571-2.6560.2821070.21918940.222228687.533
2.656-2.7490.2771070.21819910.222229891.297
2.749-2.8530.2881110.20819160.212214994.323
2.853-2.9690.326960.20819660.213211697.448
2.969-3.1010.286830.19618460.2194599.177
3.101-3.2520.2791040.19218440.196195099.897
3.252-3.4280.29910.17517260.181181899.945
3.428-3.6360.26740.16516350.169171199.883
3.636-3.8860.221830.15215550.156163999.939
3.886-4.1970.281700.15214020.1581472100
4.197-4.5970.171860.13812970.141383100
4.597-5.1390.196630.14211930.145125899.841
5.139-5.9320.295570.17510420.1811099100
5.932-7.2610.274530.1878770.192930100
7.261-10.2480.17360.1566920.156728100
10.248-117.0410.16200.1643690.16439698.232
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)
15.2393-0.1057-1.42963.1970.1322.6860.1914-0.1360.21180.128-0.0774-0.116-0.1249-0.0161-0.1141-0.16640.0130.0024-0.2067-0.0464-0.281327.44834.8371.34
24.9259-0.17671.25013.4145-0.16092.47910.1888-0.1725-0.22770.0913-0.06720.11490.1323-0.0053-0.1216-0.16520.0156-0.0053-0.16530.0418-0.285140.0884.2171.337
37.2854-2.73131.68544.1334-1.70865.73970.5472-0.01360.6873-0.0195-0.0762-0.5259-0.81290.2888-0.47110.0764-0.10380.1954-0.121-0.05370.124440.99850.658-6.427
47.2568-2.5602-2.9635.61513.13954.7670.4022-0.2796-0.7658-0.0501-0.05390.59030.7322-0.2779-0.34840.1219-0.1064-0.2111-0.04110.10910.089526.59-11.612-6.416
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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