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- PDB-2jga: Crystal structure of human cytosolic 5'-nucleotidase III in compl... -

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Basic information

Entry
Database: PDB / ID: 2jga
TitleCrystal structure of human cytosolic 5'-nucleotidase III in complex with phosphate and magnesium
ComponentsCYTOSOLIC 5'-NUCLEOTIDASE III
KeywordsHYDROLASE / PYRIMIDINE 5-PRIME- NUCLEOTIDASE 1 / NUCLEOTIDE METABOLISM / PYRIMIDINE 5-PRIME NUCLEOTIDASE DEFICIENCY / URIDINE 5-PRIME MONOPHOSPHATE HYDROLASE 1 / CYTOSOLIC III / DISEASE MUTATION / NUCLEOTIDE-BINDING / P5N1 / UMPH1 / 5-PRIME / NUCLEOTIDASE
Function / homology
Function and homology information


pyrimidine nucleoside metabolic process / tRNA 2'-phosphotransferase activity / 7-methylguanosine nucleotidase / Pyrimidine catabolism / 5'-nucleotidase / 5'-nucleotidase activity / nucleotide metabolic process / defense response to virus / nuclear body / nucleotide binding ...pyrimidine nucleoside metabolic process / tRNA 2'-phosphotransferase activity / 7-methylguanosine nucleotidase / Pyrimidine catabolism / 5'-nucleotidase / 5'-nucleotidase activity / nucleotide metabolic process / 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
PHOSPHATE ION / Cytosolic 5'-nucleotidase 3A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsWallden, K. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. ...Wallden, K. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, M. / Holmberg, B. / Schiavone, L. / Hogbom, M. / Kotenyova, T. / Magnusdottir, A. / Nilsson-Ehle, P. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Sundstrom, M. / Thorsell, A.G. / Uppenberg, J. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Nordlund, P.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal Structure of Human Cytosolic 5'-Nucleotidase II: Insights Into Allosteric Regulation and Substrate Recognition.
Authors: Wallden, K. / Stenmark, P. / Nyman, T. / Flodin, S. / Graslund, S. / Loppnau, P. / Bianchi, V. / Nordlund, P.
History
DepositionFeb 9, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr2_label_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3463
Polymers33,2271
Non-polymers1192
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)87.459, 101.036, 77.046
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein CYTOSOLIC 5'-NUCLEOTIDASE III / CN-III / PYRIMIDINE 5'-NUCLEOTIDASE 1 / P5'N-1 / P5N-1 / PN-I / URIDINE 5'-MONOPHOSPHATE HYDROLASE 1 / P36


Mass: 33227.035 Da / Num. of mol.: 1 / Fragment: RESIDUES 14-286
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H0P0, 5'-nucleotidase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsISOFORM 2

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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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growDetails: 24% PEG1500 AND 20% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9196
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 22, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9196 Å / Relative weight: 1
ReflectionResolution: 3→77.15 Å / Num. obs: 7057 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 12.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 24.1
Reflection shellResolution: 3→3.16 Å / Redundancy: 13 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 6.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0021refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CN1

2cn1


Resolution: 3.01→50.19 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.878 / SU B: 37.473 / SU ML: 0.339 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.472 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.268 335 4.8 %RANDOM
Rwork0.181 ---
obs0.185 6706 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2--0.23 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 3.01→50.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2190 0 6 15 2211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222232
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.9743012
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9295272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.73225.421107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.56915420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.697159
X-RAY DIFFRACTIONr_chiral_restr0.0880.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021654
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.2950
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21520
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.274
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.213
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4481.51382
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.79722193
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.293937
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.174.5819
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.01→3.08 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.383 27
Rwork0.199 469
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)
19.99183.0487-3.50469.2083-6.46484.74580.5696-0.5691-0.02251.7609-0.0961-0.0651-0.24490.6838-0.47350.04270.0359-0.00740.1818-0.08250.043223.69977.157738.1212
21.80110.1256-1.12241.5934-0.27952.73610.04210.27060.2015-0.38290.03580.0972-0.0979-0.0285-0.07790.15220.0692-0.08440.171-0.02150.156631.52912.040310.8581
30.1859-0.3784-1.63869.29392.227314.58840.13310.3607-0.0834-0.53820.4062-0.3271-0.36231.6368-0.5393-0.06170.09640.09490.34650.09440.280438.695626.143-1.5286
41.54180.17370.36564.62631.81184.56880.02940.18680.52650.20780.20160.5201-0.1814-0.0242-0.23090.11050.07890.05290.05820.1190.253830.1827.87046.7653
54.77050.8022-2.23491.9942-0.57778.8639-0.07620.1313-0.42-0.43660.0772-0.02180.9793-0.0704-0.0010.19780.0255-0.0531-0.0473-0.09140.149727.13452.452812.3072
60.2860.6253-0.7965.0778-2.18742.2696-0.0580.70880.1756-0.4750.1890.25220.3862-0.7188-0.1310.08820.0004-0.18370.21450.01340.172619.396111.6827.5043
77.48452.92514.48445.8131-1.00347.6999-0.26750.20680.9228-0.00620.11030.87940.097-0.76280.1572-0.01330.1368-0.0580.06620.14850.241920.199624.69325.8479
85.11611.3055-2.08634.1115-1.96543.74960.37380.10970.62220.38460.07830.8845-0.3722-0.5956-0.4520.07050.07760.05450.0579-0.04120.255316.974618.071623.7997
910.65532.2677-2.95243.7993-1.34781.72320.601-0.51170.48630.5001-0.3591-0.0918-0.46180.2298-0.24190.1376-0.00290.00160.11-0.0622-0.043634.605317.961927.4671
106.50342.742-2.25642.0679-2.23413.0271-0.1963-0.2325-0.72940.0525-0.1571-0.37730.30210.27370.35340.11340.0479-0.05470.1063-0.03790.114730.61995.596926.7956
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 30
2X-RAY DIFFRACTION2A31 - 66
3X-RAY DIFFRACTION3A67 - 80
4X-RAY DIFFRACTION4A81 - 121
5X-RAY DIFFRACTION5A122 - 145
6X-RAY DIFFRACTION6A146 - 188
7X-RAY DIFFRACTION7A189 - 199
8X-RAY DIFFRACTION8A200 - 242
9X-RAY DIFFRACTION9A243 - 264
10X-RAY DIFFRACTION10A265 - 286

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