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- PDB-5opm: Crystal structure of D52N/R238W cN-II mutant bound to dATP and fr... -

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Basic information

Entry
Database: PDB / ID: 5opm
TitleCrystal structure of D52N/R238W cN-II mutant bound to dATP and free phosphate
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 catabolic process / IMP metabolic 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 / 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
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / PHOSPHATE ION / Cytosolic purine 5'-nucleotidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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 ...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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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)56,3559
Polymers55,3521
Non-polymers1,0038
Water6,323351
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)225,42236
Polymers221,4094
Non-polymers4,01332
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area17260 Å2
ΔGint-118 kcal/mol
Surface area76040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.087, 127.454, 130.948
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / Cytosolic 5'-nucleotidase II


Mass: 55352.281 Da / Num. of mol.: 1 / Mutation: D52N/R238W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NT5C2, NT5B, NT5CP, PNT5 / Production host: Escherichia coli (E. coli) / References: UniProt: P49902, 5'-nucleotidase

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Non-polymers , 5 types, 359 molecules

#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.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 3.47 Å3/Da / Density % sol: 64.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M bicine/Trizma base pH 8.5; 0.02 M of each amino acid; 10% w/v PEG 4000, 20% v/v glycerol H11 Morpheus condition

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.677→45.67 Å / Num. obs: 84931 / % possible obs: 99.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 28.767 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.068 / Net I/σ(I): 14.5
Reflection shellResolution: 1.68→1.78 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 1.95 / Num. unique obs: 13693 / CC1/2: 0.663 / Rrim(I) all: 0.751 / % possible all: 97.3

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Processing

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

5k7y


Resolution: 1.68→45.67 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.075
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1966 2101 2.4 %RANDOM
Rwork0.1779 ---
obs0.1784 84931 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 104.7 Å2 / Biso mean: 29.173 Å2 / Biso min: 13.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.68→45.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3825 0 61 351 4237
Biso mean--35.7 32.34 -
Num. residues----469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194025
X-RAY DIFFRACTIONr_bond_other_d00.023765
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.9725445
X-RAY DIFFRACTIONr_angle_other_deg3.58238673
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1245481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94223190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59915692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5771527
X-RAY DIFFRACTIONr_chiral_restr0.0910.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024456
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02986
LS refinement shellResolution: 1.677→1.721 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 147 -
Rwork0.32 5916 -
all-6063 -
obs--94.42 %
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)
13.64055.77720.28449.19390.53868.57420.08520.12590.34910.13980.25380.4752-0.5003-0.042-0.33910.37570.0261-0.03340.36320.01630.3905-0.78135.79435.083
222.657915.627-2.548411.7608-2.21520.5038-0.0464-0.03331.76150.1346-0.08710.4975-0.11440.00440.13350.691-0.0369-0.03580.6467-0.02760.679911.59141.43731.519
35.33838.2628-3.500212.9458-5.70385.70360.10030.3250.44950.24650.28370.4692-0.61990.0048-0.3840.5111-0.01830.03280.58270.18580.663712.95247.86441.865
43.6356-1.448-1.29591.63260.81171.760.0812-0.10910.4085-0.028-0.0017-0.2415-0.26390.2258-0.07960.1828-0.0650.00640.14270.00620.070214.44635.96753.379
51.23540.1822-0.28850.3979-0.08740.6816-0.05820.1554-0.0107-0.09410.03140.05410.0086-0.12440.02670.1152-0.0031-0.01970.13390.00540.0115-10.72219.96942.405
61.54821.5081-0.83062.7241.517.0975-0.0061-0.02210.1330.0667-0.05370.1937-0.0305-0.28530.05990.15360.01570.00010.1575-0.0120.0439-18.91120.93259.045
73.39321.3124-0.09512.46710.09021.4292-0.09680.1778-0.1331-0.03030.08130.18550.0284-0.13940.01550.08960.0182-0.01090.1179-0.00680.0368-18.715.19443.896
84.63881.3063-2.29021.7487-0.82551.2138-0.0980.0506-0.2263-0.04540.03490.05250.0640.010.0630.13040.0118-0.02080.1462-0.01420.0792-14.1917.63344.293
93.032.2584-1.398.4652-0.75621.6816-0.14520.4242-0.1923-0.28340.1035-0.02740.0398-0.07480.04170.1183-0.0040.01230.2133-0.00790.042.41818.75629.829
106.9259-2.50264.58366.2437-4.79178.13690.25880.17590.2469-0.3836-0.1877-0.31150.04870.2903-0.07120.191-0.02520.05170.14460.01340.060220.60132.23140.183
111.43870.5432-0.6910.7219-0.79991.6173-0.0150.16580.0332-0.10370.0063-0.0462-0.01440.04870.00860.1369-0.01740.04180.15410.01630.017117.30822.9134.248
121.2674-0.3702-0.41472.65210.80371.1472-0.00490.0135-0.0296-0.0846-0.0053-0.08540.02760.06910.01020.1085-0.03190.00910.13060.0230.009712.67519.13948.572
1313.6367-0.1786-10.22141.7843-1.554412.6658-0.0111-0.18230.14010.22740.01490.5182-0.7079-0.373-0.00370.55440.1339-0.05760.3849-0.00550.5391-18.96346.36360.006
142.98250.69390.10821.57130.32591.7732-0.0028-0.03070.3439-0.1204-0.02190.1813-0.2262-0.14090.02470.17460.0203-0.01910.08580.00760.0497-3.0135.85551.66
152.60510.2465-5.56740.148-0.235612.5910.2820.06120.20330.01490.08680.028-0.62530.0371-0.36890.2803-0.0030.04840.25030.02990.23055.20541.23270.304
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 12
2X-RAY DIFFRACTION2A13 - 18
3X-RAY DIFFRACTION3A19 - 32
4X-RAY DIFFRACTION4A33 - 49
5X-RAY DIFFRACTION5A50 - 125
6X-RAY DIFFRACTION6A126 - 151
7X-RAY DIFFRACTION7A152 - 186
8X-RAY DIFFRACTION8A187 - 209
9X-RAY DIFFRACTION9A210 - 229
10X-RAY DIFFRACTION10A230 - 244
11X-RAY DIFFRACTION11A245 - 286
12X-RAY DIFFRACTION12A287 - 385
13X-RAY DIFFRACTION13A386 - 421
14X-RAY DIFFRACTION14A422 - 477
15X-RAY DIFFRACTION15A478 - 488

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