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- PDB-5opn: Crystal structure of R39Q cN-II mutant -

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Basic information

Entry
Database: PDB / ID: 5opn
TitleCrystal structure of R39Q cN-II mutant
ComponentsCytosolic purine 5'-nucleotidase
KeywordsHYDROLASE / nucleotidase / relapsed leukemia
Function / homology
Function and homology information


nucleoside phosphotransferase / nucleoside phosphotransferase activity / dGMP metabolic process / GMP metabolic process / Abacavir metabolism / negative regulation of defense response to virus by host / GMP 5'-nucleotidase activity / adenosine metabolic process / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity ...nucleoside phosphotransferase / nucleoside phosphotransferase activity / dGMP metabolic process / GMP metabolic process / Abacavir metabolism / negative regulation of defense response to virus by host / GMP 5'-nucleotidase activity / adenosine metabolic process / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity / Ribavirin ADME / IMP metabolic process / IMP catabolic process / Purine catabolism / allantoin metabolic process / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / protein K48-linked ubiquitination / ubiquitin protein ligase activity / ATP binding / identical protein binding / metal ion 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: 1.77 Å
AuthorsHnizda, A. / Pachl, P. / Rezacova, P.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science Foundation15-06582S Czech Republic
CitationJournal: Leukemia / Year: 2018
Title: Relapsed acute lymphoblastic leukemia-specific mutations in NT5C2 cluster into hotspots driving intersubunit stimulation.
Authors: Hnizda, A. / Fabry, M. / Moriyama, T. / Pachl, P. / Kugler, M. / Brinsa, V. / Ascher, D.B. / Carroll, W.L. / Novak, P. / Zaliova, M. / Trka, J. / Rezacova, P. / Yang, J.J. / Veverka, V.
History
DepositionAug 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 25, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rrim_I_all
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytosolic purine 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8487
Polymers55,2951
Non-polymers5536
Water4,900272
1
A: Cytosolic purine 5'-nucleotidase
hetero molecules

A: Cytosolic purine 5'-nucleotidase
hetero molecules

A: Cytosolic purine 5'-nucleotidase
hetero molecules

A: Cytosolic purine 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,39128
Polymers221,1814
Non-polymers2,21024
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area18810 Å2
ΔGint-51 kcal/mol
Surface area76440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.469, 127.115, 130.218
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Cytosolic purine 5'-nucleotidase / Cytosolic 5'-nucleotidase II


Mass: 55295.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NT5C2, NT5B, NT5CP, PNT5 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P49902, 5'-nucleotidase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O

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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: 3.42 Å3/Da / Density % sol: 64.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M MES/imidazole pH 6.5; 0.02 M of each carboxylic acid; 10% w/v PEG 20 000, 20% v/v PEG MME 550 G1 Morpheus condition

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.766→48.45 Å / Num. obs: 73833 / % possible obs: 99.1 % / Redundancy: 4.6 % / Biso Wilson estimate: 30.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.063 / Net I/σ(I): 16.7
Reflection shellResolution: 1.77→1.87 Å / Redundancy: 3.81 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 1.91 / Num. unique obs: 11758 / CC1/2: 0.719 / Rrim(I) all: 0.71 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
PDB_EXTRACT3.22data extraction
MOLREPphasing
XDSdata reduction
Cootmodel building
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K7Y

5k7y


Resolution: 1.77→48.45 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.087
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2001 2100 2.8 %RANDOM
Rwork0.1793 ---
obs0.1799 71727 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 97.37 Å2 / Biso mean: 30.749 Å2 / Biso min: 16.08 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.77→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3843 0 36 274 4153
Biso mean--46.54 33.79 -
Num. residues----472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194030
X-RAY DIFFRACTIONr_bond_other_d00.023791
X-RAY DIFFRACTIONr_angle_refined_deg1.491.9655444
X-RAY DIFFRACTIONr_angle_other_deg3.59838744
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0265489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.25723.175189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90315699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0041525
X-RAY DIFFRACTIONr_chiral_restr0.0950.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024488
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02981
LS refinement shellResolution: 1.766→1.812 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 151 -
Rwork0.33 5167 -
all-5318 -
obs--98.06 %
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)
17.06775.4965-0.50995.6013-1.08860.7710.127-0.0457-0.416-0.1024-0.00840.00130.1865-0.015-0.11870.23680.0125-0.02590.222-0.02640.1804-8.748-41.906-28.222
25.0593-0.71690.4151.5613-1.24492.99640.0230.0885-0.5743-0.02580.04240.25390.4993-0.013-0.06540.1992-0.0497-0.02620.16790.01480.1318-12.287-39.085-13.837
31.40590.48560.08440.46640.01270.6625-0.05390.07640.0718-0.09010.0345-0.0130.01530.07670.01950.05320.01060.01130.1035-0.00050.009910.531-20.126-22.68
43.51751.04540.75263.5721-1.82256.5820.0052-0.2158-0.10420.149-0.0383-0.17040.12690.17190.03310.0993-0.00580.0020.1086-0.01150.012618.563-20.238-5.905
54.78131.74280.91583.02460.2291.7094-0.08360.25840.2247-0.05240.0651-0.1993-0.09180.12010.01850.05950.02180.00830.08420.01920.045719.785-14.401-22.02
63.81131.94831.96262.00581.23691.5798-0.16540.1630.3714-0.13280.03530.1667-0.1245-0.04680.13020.08060.01640.00980.14540.03870.04976.149-12.622-28.006
71.20490.14980.37211.09450.80882.72990.0133-0.0388-0.0270.0311-0.01660.02720.1147-0.04530.00330.0506-0.0117-0.0270.1085-0.00290.0184-17.084-23.24-27.23
82.07150.63360.87764.2015-1.20083.8726-0.0596-0.01060.0954-0.04870.09120.372-0.3213-0.105-0.03170.11490.0038-0.01450.1473-0.04740.1053-21.929-9.599-20.42
93.0099-0.8167-0.56211.7701-0.02261.71380.0235-0.1118-0.0768-0.0238-0.0085-0.25140.20350.1011-0.01490.101-0.0218-0.01280.13840.00520.053-1.669-32.088-13.156
108.7592-4.6450.99462.5248-0.10924.56210.2920.498-0.3671-0.0571-0.2110.14370.106-0.2116-0.08110.68750.1148-0.0880.6021-0.03250.596623.09-46.484-1.146
113.02020.8035-0.30951.3564-0.32341.97230.0261-0.2317-0.3637-0.1223-0.0451-0.15730.23960.09510.0190.12630.02020.00110.07950.01910.04842.846-35.624-13.792
124.13310.61257.70730.11881.123814.38510.32160.1052-0.19170.01360.0720.01220.62470.1672-0.39350.2761-0.0119-0.07120.2298-0.02820.1968-5.12-40.8964.773
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 27
2X-RAY DIFFRACTION2A28 - 47
3X-RAY DIFFRACTION3A48 - 127
4X-RAY DIFFRACTION4A128 - 152
5X-RAY DIFFRACTION5A153 - 188
6X-RAY DIFFRACTION6A189 - 228
7X-RAY DIFFRACTION7A229 - 297
8X-RAY DIFFRACTION8A298 - 342
9X-RAY DIFFRACTION9A343 - 396
10X-RAY DIFFRACTION10A397 - 421
11X-RAY DIFFRACTION11A422 - 477
12X-RAY DIFFRACTION12A478 - 488

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