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- PDB-2j2c: Crystal structure of Human Cytosolic 5'-Nucleotidase II (NT5C2, cN-II) -

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Basic information

Entry
Database: PDB / ID: 2j2c
TitleCrystal structure of Human Cytosolic 5'-Nucleotidase II (NT5C2, cN-II)
ComponentsCYTOSOLIC PURINE 5'-NUCLEOTIDASE
KeywordsHYDROLASE / CYTOSOLIC 5-PRIME NUCLEOTIDASE II / ALLOSTERIC ENZYME / GMP- IMP SPECIFIC NUCLEOTIDASE / HIGH KM 5-PRIME NUCLEOTIDASE / CN- II / NT5C2 / CYTOSOLIC PURINE 5- PRIME NUCLEOTIDASE
Function / homology
Function and homology information


nucleoside phosphotransferase / GMP catabolic process to guanine / nucleoside phosphotransferase activity / GMP metabolic process / : / Abacavir metabolism / dGMP metabolic process / negative regulation of defense response to virus by host / dGMP catabolic process / adenosine metabolic process ...nucleoside phosphotransferase / GMP catabolic process to guanine / nucleoside phosphotransferase activity / GMP metabolic process / : / Abacavir metabolism / dGMP metabolic process / negative regulation of defense response to virus by host / dGMP catabolic process / adenosine metabolic process / : / amide catabolic process / IMP-specific 5'-nucleotidase / : / IMP catabolic process / Ribavirin ADME / IMP metabolic process / Purine catabolism / 5'-nucleotidase / allantoin metabolic process / 5'-nucleotidase activity / protein K48-linked ubiquitination / ubiquitin protein ligase activity / ATP binding / metal ion binding / identical protein binding / cytoplasm / cytosol
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
Cytosolic purine 5'-nucleotidase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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. / Loppnau, P. / Magnusdottir, A. / Nilsson-Ehle, P. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Sundstrom, M. / Uppenberg, J. / Thorsell, A.G. / 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
DepositionAug 16, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 4, 2020Group: Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.3Dec 13, 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
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.pdbx_dist_value / _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 PURINE 5'-NUCLEOTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7829
Polymers64,0891
Non-polymers6938
Water8,017445
1
A: CYTOSOLIC PURINE 5'-NUCLEOTIDASE
hetero molecules

A: CYTOSOLIC PURINE 5'-NUCLEOTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,56318
Polymers128,1782
Non-polymers1,38616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
Buried area7610 Å2
ΔGint-206 kcal/mol
Surface area39830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.465, 128.034, 130.415
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


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 / Cell line (production host): ROSETTA2(DE) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P49902, 5'-nucleotidase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsOUR CONSTRUCT CONTAINS RESIDUES 1-536 OUT OF THE 561 AMINO ACIDS. ADDITIONALLY IT CONTAINS AN N- ...OUR CONSTRUCT CONTAINS RESIDUES 1-536 OUT OF THE 561 AMINO ACIDS. ADDITIONALLY IT CONTAINS AN N-TERMINAL HISTAG MGSSHHHHHHSSGLVPRGS

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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: 3.17 Å3/Da / Density % sol: 61.17 %
Crystal growDetails: 1.8 M MG2SO4 0.1 M TRIS PH 8.5

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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 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9196 Å / Relative weight: 1
ReflectionResolution: 2.2→91.29 Å / Num. obs: 39212 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 11.5 / % possible all: 100

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Processing

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

2bde


Resolution: 2.2→40 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.989 / SU ML: 0.085 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 3-400 AND 417-488 OUT OF 536 RESIDUES ARE MODELLED
RfactorNum. reflection% reflectionSelection details
Rfree0.184 1967 5 %RANDOM
Rwork0.152 ---
obs0.154 37234 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3828 0 37 445 4310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224058
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.975501
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9585494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.77923.265196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.10215707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4381527
X-RAY DIFFRACTIONr_chiral_restr0.1010.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023101
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.21794
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22744
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2391
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7721.52487
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20623873
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.10531832
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1714.51621
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: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.208 135
Rwork0.149 2730
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)
15.9933.71120.34845.44181.34211.84-0.0218-0.03870.4494-0.2440.04060.1084-0.2665-0.0127-0.01880.17530.0115-0.0041-0.06690.0587-0.05487.71542.68438.406
20.77730.22150.05690.44170.08990.53110.02050.0470.0031-0.0313-0.00020.0059-0.0335-0.0179-0.02030.09770.0098-0.0088-0.04890.016-0.0735-6.26122.66644.09
30.96581.74611.43634.06880.81665.6126-0.1522-0.10210.18890.0738-0.16780.2563-0.2406-0.60720.320.10210.01460.00590.0284-0.027-0.0768-20.67622.27259.573
41.02630.4045-1.19281.6961-0.16471.4471-0.05740.1018-0.09460.05390.05860.06310.04280.0308-0.00120.10250.031-0.0161-0.0590.0055-0.0466-16.31915.72144.967
54.53912.3003-2.15882.0468-1.08331.5007-0.13340.1151-0.2089-0.05350.0766-0.05850.1462-0.00640.05670.11210.0105-0.0473-0.0294-0.0183-0.0675-9.79712.17739.02
61.17070.6668-0.37460.9665-0.52781.10340.02110.08620.0374-0.0173-0.0297-0.0436-0.12770.0610.00860.1028-0.01340.0343-0.02870.0155-0.041818.03425.01535.757
71.1463-0.8343-0.49452.18640.46210.4594-0.0102-0.0061-0.0464-0.0573-0.0139-0.05760.06980.07480.02410.0885-0.02140.015-0.0270.0194-0.080113.94917.88348.702
814.2793-2.3561-11.03014.28875.169321.70340.20.21020.60140.341-0.07780.1221-1.2277-1.3459-0.12220.23090.2248-0.067-0.05050.00310.0492-17.18145.81956.057
91.33740.44710.21580.98690.21771.8068-0.0265-0.07390.1574-0.0639-0.01880.0942-0.21440.0130.04530.1290.0063-0.0073-0.09660.006-0.0618-1.17235.48150.943
105.07931.0924-10.75950.85460.096532.16810.58670.02850.3887-0.27570.1601-0.233-1.49120.2761-0.74680.27240.00750.066-0.02760.03830.08915.11141.22870.186
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 34
2X-RAY DIFFRACTION2A35 - 125
3X-RAY DIFFRACTION3A126 - 146
4X-RAY DIFFRACTION4A147 - 179
5X-RAY DIFFRACTION5A180 - 229
6X-RAY DIFFRACTION6A230 - 288
7X-RAY DIFFRACTION7A289 - 381
8X-RAY DIFFRACTION8A382 - 424
9X-RAY DIFFRACTION9A425 - 477
10X-RAY DIFFRACTION10A478 - 488

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