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- PDB-5opo: Crystal structure of R238G cN-II mutant -

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Basic information

Entry
Database: PDB / ID: 5opo
TitleCrystal structure of R238G 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: 2 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 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 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)56,7939
Polymers56,1241
Non-polymers6698
Water8,287460
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)227,17236
Polymers224,4964
Non-polymers2,67632
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 area20170 Å2
ΔGint-73 kcal/mol
Surface area76780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.612, 126.862, 130.572
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: 56124.039 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.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 460 / 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: 3.38 Å3/Da / Density % sol: 63.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M MOPS/HEPES-Na pH 7.5; 0.03 M of each divalent cation ; 10% w/v PEG 4000, 20% v/v glycerol A7 Morpheus condition

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.894 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.894 Å / Relative weight: 1
ReflectionResolution: 1.969→48.43 Å / Num. obs: 54032 / % possible obs: 99.8 % / Redundancy: 4.6 % / Biso Wilson estimate: 30.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.112 / Net I/σ(I): 13.6
Reflection shellResolution: 1.97→2.09 Å / Redundancy: 4.58 % / Rmerge(I) obs: 0.751 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 8599 / CC1/2: 0.703 / Rrim(I) all: 0.849 / % possible all: 99.3

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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: 2→48.43 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.123
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 2100 4.1 %RANDOM
Rwork0.1708 ---
obs0.1721 49530 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 94.54 Å2 / Biso mean: 32.031 Å2 / Biso min: 11.98 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3858 0 43 467 4368
Biso mean--55.4 30.12 -
Num. residues----474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194082
X-RAY DIFFRACTIONr_bond_other_d00.023849
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.9665518
X-RAY DIFFRACTIONr_angle_other_deg3.58338883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3265500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.26823.128195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02215713
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5461527
X-RAY DIFFRACTIONr_chiral_restr0.0910.2591
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024547
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02994
LS refinement shellResolution: 1.999→2.051 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 150 -
Rwork0.288 3552 -
all-3702 -
obs--99.36 %
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)
18.31936.2999-0.5176.2575-0.78520.2529-0.00080.2459-0.4944-0.16530.0962-0.05390.23870.0274-0.09540.3857-0.0022-0.02850.2601-0.08010.2625-5.268-38.215-30.96
210.755911.31755.536212.2524.43838.89790.2285-0.1746-0.97980.0185-0.1941-1.02381.24280.0141-0.03430.4770.04670.10260.3441-0.03030.7537-11.155-47.199-22.052
31.66980.37680.16050.4717-0.0350.9047-0.03290.10640.0336-0.07350.0275-0.00830.04660.04710.00540.0590.00880.0110.0235-0.00790.01396.565-22.457-20.731
45.27863.3154-1.76484.8092-0.79969.1392-0.1236-0.0266-0.41810.0658-0.0849-0.47040.54540.70510.20860.16480.0154-0.00120.10430.00370.061621.47-22.921-4.882
53.45761.27660.67882.62820.41642.0927-0.10630.17130.25230.01040.0939-0.0578-0.07620.03410.01240.05390.02430.01140.03180.0250.045317.796-14.633-19.401
66.57550.74783.79352.52130.21022.96530.0103-0.16170.3476-0.035-0.00350.1626-0.0475-0.2844-0.00690.11160.04970.03230.09740.02790.118312.919-7.211-21.906
74.16811.0193-0.81561.89070.20742.354-0.15390.4715-0.0046-0.1590.14160.00260.2267-0.15140.01220.1267-0.008-0.05370.10780.00310.0392-11.7-25.009-30.191
82.27180.97290.60831.34010.99372.0698-0.04860.149-0.0095-0.12120.04370.0112-0.04250.01250.00480.0663-0.0122-0.03780.0667-0.00550.0279-17.1-21.955-31.154
90.9061-0.82030.74292.8575-1.0421.6841-0.0954-0.06020.13740.00940.05890.1706-0.244-0.12180.03640.1023-0.0233-0.01760.1008-0.02640.0691-16.055-15.593-15.836
103.8547-2.83713.61863.6581-1.88795.30040.21680.152-0.42580.0292-0.1087-0.19580.86320.3209-0.1080.32380.05920.10180.1660.02660.412710.141-42.825-14.436
1129.793.1686-23.97581.0264-1.494120.9235-0.37570.78910.34810.1130.42610.17350.5148-0.1469-0.05040.28060.0616-0.09240.37210.04050.29926.966-47.149-0.197
122.63680.8354-0.74751.7106-0.24092.3117-0.0156-0.1612-0.2761-0.0982-0.0169-0.19150.2580.15810.03240.13280.02810.01010.02630.0060.04534.111-35.931-13.525
132.42811.29164.21560.72731.866111.36750.1079-0.0094-0.07170.03130.0192-0.02580.2046-0.1527-0.12710.18630.0131-0.02810.1397-0.01560.1712-5.218-40.9634.781
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 20
2X-RAY DIFFRACTION2A21 - 34
3X-RAY DIFFRACTION3A35 - 127
4X-RAY DIFFRACTION4A128 - 145
5X-RAY DIFFRACTION5A146 - 186
6X-RAY DIFFRACTION6A187 - 212
7X-RAY DIFFRACTION7A213 - 248
8X-RAY DIFFRACTION8A249 - 290
9X-RAY DIFFRACTION9A291 - 371
10X-RAY DIFFRACTION10A372 - 399
11X-RAY DIFFRACTION11A400 - 419
12X-RAY DIFFRACTION12A420 - 477
13X-RAY DIFFRACTION13A478 - 488

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