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- PDB-2bdu: X-Ray Structure of a Cytosolic 5'-Nucleotidase III from Mus Muscu... -

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Basic information

Entry
Database: PDB / ID: 2bdu
TitleX-Ray Structure of a Cytosolic 5'-Nucleotidase III from Mus Musculus MM.158936
ComponentsCytosolic 5'-nucleotidase III
KeywordsHYDROLASE / UMPH-1 / CYTOSOLIC 5'-NUCLEOTIDASE III / NT5C3 PROTEIN / AAH38029 / BC038029 / MM.158936 / STRUCTURAL GENOMICS / 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 ...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
Cytosolic 5'-nucleotidase 3A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2.35 Å
AuthorsWesenberg, G.E. / Phillips Jr., G.N. / Han, B.W. / Bitto, E. / Bingman, C.A. / Bae, E. / 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
DepositionOct 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.pdbx_leaving_atom_flag / _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

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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)68,8044
Polymers68,3282
Non-polymers4772
Water6,467359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.674, 133.674, 38.889
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

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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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 3 Å3/Da / Density % sol: 58.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10 MG/ML PROTEIN, 26% PEG 8K, 0.10 M MOPS (HEPES USED AS CRYOPROTECTANT), pH 7.0, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97911 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 10, 2005
Details: HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR
RadiationMonochromator: CRYOGENICALLY COOLED SI (220) DOUBLE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionRedundancy: 5.4 % / Number: 31917 / Rmerge(I) obs: 0.091 / Χ2: 0.991 / D res high: 2.35 Å / D res low: 50 Å / % possible obs: 98.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.795099.810.0711.0195.9
4.65.7910010.0710.9165.9
4.024.610010.0730.8715.9
3.654.0210010.0780.925.9
3.393.6599.910.0840.8545.9
3.193.3999.910.0991.115.9
3.033.1910010.1221.1485.9
2.93.0399.710.1531.0615.8
2.792.910010.1821.2185.9
2.692.7999.510.2231.0465.7
2.612.6910010.2571.0265.7
2.532.6198.910.310.8945.2
2.462.5398.910.3350.8734.6
2.42.4693.310.350.8643.9
2.352.487.810.3670.8853.3
ReflectionResolution: 2.35→43.755 Å / Num. obs: 31917 / % possible obs: 98.5 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.091 / Χ2: 0.991 / Net I/σ(I): 6.818
Reflection shellResolution: 2.35→2.4 Å / % possible obs: 87.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 2.067 / Num. measured obs: 1921 / Χ2: 0.885 / % possible all: 87.8

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Phasing

PhasingMethod: MAD
Phasing MAD set

R cullis centric: 0 / Highest resolution: 2.35 Å / Lowest resolution: 43.76 Å / Power centric: 0 / Reflection centric: _

IDR cullis acentricPower acentricReflection acentric
ISO_10031781
ANO_10.8251.10630198
Phasing MAD set shell

R cullis centric: 0 / Power centric: 0 / Reflection centric: _

IDResolution (Å)R cullis acentricPower acentricReflection acentric
ISO_110.24-43.7600378
ISO_17.35-10.2400661
ISO_16.03-7.3500869
ISO_15.23-6.03001017
ISO_14.69-5.23001150
ISO_14.28-4.69001261
ISO_13.97-4.28001378
ISO_13.71-3.97001490
ISO_13.5-3.71001561
ISO_13.32-3.5001662
ISO_13.17-3.32001729
ISO_13.03-3.17001822
ISO_12.92-3.03001912
ISO_12.81-2.92001985
ISO_12.72-2.81002062
ISO_12.63-2.72002102
ISO_12.55-2.63002194
ISO_12.48-2.55002252
ISO_12.41-2.48002156
ISO_12.35-2.41002140
ANO_110.24-43.760.8371.413378
ANO_17.35-10.240.761.396661
ANO_16.03-7.350.6121.818869
ANO_15.23-6.030.6751.7591017
ANO_14.69-5.230.7331.51149
ANO_14.28-4.690.7681.3821257
ANO_13.97-4.280.7851.2361378
ANO_13.71-3.970.7611.2481484
ANO_13.5-3.710.8031.2621553
ANO_13.32-3.50.791.21661
ANO_13.17-3.320.8021.1731713
ANO_13.03-3.170.8460.9911822
ANO_12.92-3.030.8740.8621889
ANO_12.81-2.920.8940.761985
ANO_12.72-2.810.9230.6682028
ANO_12.63-2.720.9470.5892093
ANO_12.55-2.630.9720.4852109
ANO_12.48-2.550.9850.462066
ANO_12.41-2.480.9890.3981693
ANO_12.35-2.410.9950.3351393
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-26.452-41.15-6.728SE41.721.4
2-40.402-74.555-6.723SE40.311.4
3-99.581-30.126-8.76SE56.591.23
432.705-85.647-8.684SE48.711.11
5-34.364-28.491-3.077SE62.591.12
6-32.512-87.248-3.118SE731.33
7-79.834-70.526-4.025SE44.50.83
8-46.886-43.228-8.943SE55.760.83
9-19.913-72.482-8.949SE49.270.92
1012.921-45.26-4.026SE44.690.86
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 31812
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
9.3-100630.71511
7.4-9.3610.881513
6.4-7.455.50.878571
5.72-6.458.70.87633
5.22-5.7256.50.884731
4.83-5.2259.70.908746
4.52-4.8358.20.924845
4.26-4.5256.60.923896
4.04-4.2658.70.918936
3.85-4.0459.90.919959
3.69-3.85570.9121046
3.54-3.6964.50.8881045
3.41-3.5462.90.9011127
3.3-3.4163.20.8831155
3.19-3.3650.8641207
3.1-3.19640.8631218
3.01-3.167.50.8561262
2.93-3.0167.90.8361336
2.85-2.9368.60.831330
2.79-2.85700.831333
2.72-2.7974.10.8271430
2.66-2.7276.80.8251444
2.61-2.6676.20.831451
2.55-2.6178.80.7961527
2.5-2.5581.40.7981496
2.46-2.581.80.8091549
2.41-2.4680.50.7761461
2.35-2.41850.7192054

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM5phasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1.7data extraction
PHENIXphasing
SHELXDphasing
SOLOMONphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.35→43.755 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.238 / WRfactor Rwork: 0.173 / SU B: 11.978 / SU ML: 0.151 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.216
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, SELENIUM C COEFFICIENT FOR STRUCTURE FACTOR CALCULATION SET TO -9.00, MOLPROBITY USED TO ASSIST IN FINAL MODEL BUILDING.
RfactorNum. reflection% reflectionSelection details
Rfree0.2198 1619 5.074 %RANDOM
Rwork0.163 ---
all0.1659 ---
obs0.16588 31910 98.503 %-
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: 48.154 Å2
Baniso -1Baniso -2Baniso -3
1-0.303 Å20.151 Å20 Å2
2--0.303 Å20 Å2
3----0.454 Å2
Refinement stepCycle: LAST / Resolution: 2.35→43.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4652 0 30 359 5041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224770
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9766426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4395580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.95725.446224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.22415906
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4131518
X-RAY DIFFRACTIONr_chiral_restr0.1070.2720
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023508
X-RAY DIFFRACTIONr_nbd_refined0.2070.22278
X-RAY DIFFRACTIONr_nbtor_refined0.3030.23236
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2315
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.212
X-RAY DIFFRACTIONr_mcbond_it1.37922993
X-RAY DIFFRACTIONr_mcangle_it2.41444676
X-RAY DIFFRACTIONr_scbond_it4.64562005
X-RAY DIFFRACTIONr_scangle_it6.27581750
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 positional0.0390.05
1166medium positional0.2080.5
1164tight thermal0.3480.5
1166medium thermal1.2442
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.4110.2451200.2132024243488.085
2.411-2.4770.251110.2042085232594.452
2.477-2.5490.2541100.1962130225999.159
2.549-2.6280.2611140.1962101223799.017
2.628-2.7140.2921010.1920002101100
2.714-2.8090.2531080.1791978209699.523
2.809-2.9150.2281020.17118711973100
2.915-3.0340.252800.1821858194399.743
3.034-3.1690.241000.17317311831100
3.169-3.3230.198910.1621646174099.828
3.323-3.5030.222790.14816051684100
3.503-3.7150.201740.1541485156099.936
3.715-3.9710.199750.14714401515100
3.971-4.2890.188690.13413331402100
4.289-4.6980.185750.12811651240100
4.698-5.2510.185620.15810821144100
5.251-6.0610.275540.1879721026100
6.061-7.4190.269410.193816857100
7.419-10.470.17330.138628661100
10.47-115.470.254200.1634136798.365
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)
13.9970.2167-0.90153.21480.12612.29280.1756-0.05220.274-0.0974-0.12870.1561-0.32030.0173-0.047-0.15140.01150.0254-0.15660.018-0.241737.48775.82927.384
24.03470.14450.83643.2878-0.13592.26750.1793-0.0487-0.28-0.0885-0.1337-0.15280.31690.0102-0.0455-0.14640.014-0.0271-0.1557-0.0165-0.243929.35439.93327.388
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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