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Basic information

Entry
Database: PDB / ID: 2jcm
TitleCrystal structure of Human Cytosolic 5'-Nucleotidase II in complex with beryllium trifluoride
ComponentsCYTOSOLIC PURINE 5'-NUCLEOTIDASE
KeywordsHYDROLASE / CYTOSOLIC 5-PRIME NUCLEOTIDASE II / GMP-IMP SPECIFIC NUCLEOTIDASE / CN-II / NT5C2 / CYTOSOLIC PURINE 5-PRIME NUCLEOTIDASE / ALLOSTERIC ENZYME / HIGH KM 5-PRIME NUCLEOTIDASE
Function / homology
Function and homology information


nucleoside phosphotransferase / nucleoside phosphotransferase activity / GMP metabolic process / Abacavir metabolism / dGMP metabolic process / negative regulation of defense response to virus by host / adenosine metabolic process / IMP-specific 5'-nucleotidase / Ribavirin ADME / IMP catabolic process ...nucleoside phosphotransferase / nucleoside phosphotransferase activity / GMP metabolic process / Abacavir metabolism / dGMP metabolic process / negative regulation of defense response to virus by host / adenosine metabolic process / IMP-specific 5'-nucleotidase / Ribavirin ADME / IMP catabolic process / IMP metabolic process / dGMP catabolic process / allantoin metabolic process / Purine catabolism / 5'-nucleotidase / 5'-nucleotidase activity / protein K48-linked ubiquitination / ubiquitin protein ligase activity / ATP binding / metal ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
HAD-superfamily hydrolase, subfamily IG, 5'-nucleotidase / Purine 5'-nucleotidase / 5' nucleotidase family / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / Cytosolic purine 5'-nucleotidase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWallden, K. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. ...Wallden, K. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg Schiavone, L. / Hogbom, M. / Karlberg, T. / Kotenyova, T. / Magnusdottir, A. / Nilsson-Ehle, P. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Sundstrom, M. / Uppenberg, J. / Thorsell, A.G. / Van Den Berg, S. / Loppnau, P. / 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
DepositionDec 27, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 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 / pdbx_struct_conn_angle / 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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 2.0Sep 2, 2026Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / pdbx_contact_author / pdbx_entity_nonpoly / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_contact_author.country / _pdbx_modification_feature.auth_comp_id / _pdbx_modification_feature.auth_seq_id / _pdbx_modification_feature.category / _pdbx_modification_feature.comp_id_linking_atom / _pdbx_modification_feature.label_asym_id / _pdbx_modification_feature.label_comp_id / _pdbx_modification_feature.label_seq_id / _pdbx_modification_feature.modified_residue_auth_asym_id / _pdbx_modification_feature.modified_residue_auth_comp_id / _pdbx_modification_feature.modified_residue_auth_seq_id / _pdbx_modification_feature.modified_residue_id_linking_atom / _pdbx_modification_feature.modified_residue_label_asym_id / _pdbx_modification_feature.modified_residue_label_comp_id / _pdbx_modification_feature.modified_residue_label_seq_id / _pdbx_modification_feature.modified_residue_symmetry / _pdbx_modification_feature.ref_comp_id / _pdbx_modification_feature.ref_pcm_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOSOLIC PURINE 5'-NUCLEOTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3716
Polymers64,0891
Non-polymers2825
Water4,684260
1
A: CYTOSOLIC PURINE 5'-NUCLEOTIDASE
hetero molecules

A: CYTOSOLIC PURINE 5'-NUCLEOTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,74312
Polymers128,1782
Non-polymers56510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)91.480, 128.260, 131.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CYTOSOLIC PURINE 5'-NUCLEOTIDASE / 5'-NUCLEOTIDASE CYTOSOLIC II / CYTOSOLIC 5'-NUCLEOTIDASE II


Mass: 64088.930 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-536
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: P28A-LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2(DE) / References: UniProt: P49902, 5'-nucleotidase

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Non-polymers , 5 types, 265 molecules

#2: Chemical ChemComp-UNX / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.16 Å3/Da / Density % sol: 61.13 %
Crystal growpH: 8.5 / Details: 1.8 M MAGNESIUM SULFATE, 0.1 M TRIS PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93926
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 8, 2006 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93926 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. obs: 41406 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 7.14
Reflection shellResolution: 2.15→2.2 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.36 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.3.0021refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J2C

2j2c


Resolution: 2.15→20.67 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.891 / SU B: 11.496 / SU ML: 0.157 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2089 5 %RANDOM
Rwork0.21 ---
obs0.213 39316 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2---0.47 Å20 Å2
3---0.93 Å2
Refinement stepCycle: LAST / Resolution: 2.15→20.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3812 0 12 260 4084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223947
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7592.0025336
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5575471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.18721.429154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65415650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7551527
X-RAY DIFFRACTIONr_chiral_restr0.1170.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023001
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.21767
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22654
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2239
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9161.52423
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.44923772
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.38531778
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5264.51564
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: 2.15→2.21 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.309 147
Rwork0.258 2911
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)
14.3219-2.2241-1.07764.26421.33850.9486-0.0371-0.0826-0.59410.2110.09990.10310.3925-0.2252-0.06280.21140.0229-0.0315-0.00520.0684-0.04338.533520.517926.1685
20.7561-0.21640.02640.240.06750.1883-0.0183-0.0292-0.00150.04130.00760.00570.0636-0.01960.01070.12650.0010.01410.05290.0154-0.0624-6.338741.689821.0892
30.5025-0.7454-0.07921.34040.5760.9079-0.05240.03280.02660.0014-0.03670.08510.0615-0.09070.08920.0944-0.02350.01680.04980.0182-0.0446-18.95646.722114.7417
46.1976-2.1292.66461.3437-1.03921.1707-0.12930.13190.31120.0627-0.0156-0.1047-0.11050.11350.14480.1466-0.00030.02530.0268-0.0095-0.0311-12.708556.951922.5171
51.7762-0.41160.38180.3733-0.09550.337-0.0097-0.14690.03420.0526-0.0307-0.0824-0.00430.01890.04040.12630.0184-0.02640.05460.0235-0.063514.654140.231731.0464
61.21480.7502-0.43772.34360.37990.9831-0.031-0.09060.0018-0.03290.0434-0.1923-0.0567-0.0056-0.01230.13580.0012-0.04810.01380.0334-0.043618.907955.353721.0985
71.3420.15110.07320.15960.21910.3158-0.00670.0556-0.13050.0692-0.0181-0.0147-0.00280.05060.02480.14310.0351-0.0020.05580.0147-0.05177.307536.204113.7474
83.8685-6.31450.377220.378911.040113.52551.35420.54750.1098-1.0002-1.40071.17931.2165-1.42640.04650.2507-0.00160.0280.17980.02760.2184-19.346318.48246.0138
90.9626-0.6085-0.26070.39810.25470.6688-0.03810.1333-0.09410.0935-0.01870.06150.12870.0010.05690.1638-0.0220.01560.0130.0078-0.0419-1.826829.263514.0323
101.47111.52223.14411.57523.25346.71980.35920.3348-0.1650.0668-0.0825-0.0921.27820.6382-0.27670.23860.0658-0.02530.03830.0301-0.01987.019523.1708-2.3429
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 34
2X-RAY DIFFRACTION2A35 - 125
3X-RAY DIFFRACTION3A126 - 186
4X-RAY DIFFRACTION4A187 - 212
5X-RAY DIFFRACTION5A213 - 289
6X-RAY DIFFRACTION6A290 - 331
7X-RAY DIFFRACTION7A332 - 388
8X-RAY DIFFRACTION8A389 - 424
9X-RAY DIFFRACTION9A425 - 475
10X-RAY DIFFRACTION10A476 - 488

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