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- PDB-5opk: Crystal structure of D52N/R367Q cN-II mutant bound to dATP and fr... -

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Basic information

Entry
Database: PDB / ID: 5opk
TitleCrystal structure of D52N/R367Q 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 / IMP metabolic process / Ribavirin ADME / 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 / 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: 1.74 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_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_symmetry / _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_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_symmetry

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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)56,75814
Polymers55,2941
Non-polymers1,46413
Water5,350297
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)227,03156
Polymers221,1774
Non-polymers5,85452
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 area23010 Å2
ΔGint-123 kcal/mol
Surface area76040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.579, 127.104, 130.317
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: 55294.203 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

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Non-polymers , 5 types, 310 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine triphosphate


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 3.43 Å3/Da / Density % sol: 64.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M MES/imidazole pH 6.5; 0.03 M of each divalent cation; 10% w/v PEG 8000, 20% v/v ethylene glycol (Morpheus condition A2)

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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 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.736→48.99 Å / Num. obs: 77607 / % possible obs: 98.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 29.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rrim(I) all: 0.101 / Net I/av σ(I): 13.55 / Net I/σ(I): 13.6
Reflection shellResolution: 1.74→1.84 Å / Redundancy: 6.21 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.88 / Num. unique obs: 11899 / CC1/2: 0.823 / Rrim(I) all: 0.905 / % possible all: 94.6

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Processing

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

5k7y


Resolution: 1.74→48.99 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.088
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2034 3881 5 %RANDOM
Rwork0.1785 ---
obs0.1797 73724 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 105.74 Å2 / Biso mean: 29.152 Å2 / Biso min: 3.04 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.74→48.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3843 0 91 311 4245
Biso mean--37.1 32.21 -
Num. residues----472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194187
X-RAY DIFFRACTIONr_bond_other_d00.023917
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.9785667
X-RAY DIFFRACTIONr_angle_other_deg3.59839033
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1335504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.92723.046197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1415721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7021529
X-RAY DIFFRACTIONr_chiral_restr0.0960.2600
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024683
X-RAY DIFFRACTIONr_gen_planes_other0.0150.021025
LS refinement shellResolution: 1.736→1.781 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 259 -
Rwork0.403 4905 -
all-5164 -
obs--89.82 %
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)
19.17177.8341-1.22528.2595-1.86990.92630.159-0.132-0.5105-0.1483-0.0808-0.07080.27960.0392-0.07820.3142-0.0056-0.06370.25-0.02430.231-8.961-41.815-28.2
24.2703-0.38161.4440.9307-1.34743.31490.08630.1825-0.5968-0.150.03510.15810.4764-0.0287-0.12150.1807-0.0911-0.01360.17370.00120.2196-12.206-38.724-13.633
31.19740.37950.13010.495-0.04420.6151-0.06020.13410.0624-0.08840.0365-0.06430.0150.11160.02380.02750.00380.01690.0880.00250.025410.479-19.975-22.697
42.1932.39020.32574.017-2.192510.1612-0.0728-0.2829-0.0930.2464-0.086-0.34760.08010.4470.15880.2240.1175-0.06420.2728-0.06970.096819.131-20.279-5.785
55.00011.72730.67363.08340.18021.5322-0.10270.26740.2015-0.03090.0949-0.2742-0.08850.14750.00790.03480.01820.01050.08920.02210.062819.425-14.443-21.701
64.58532.52672.42442.89991.80861.7503-0.26140.26460.4058-0.16950.09020.172-0.16040.03140.17110.05410.00170.00670.13650.06010.06426.134-12.403-27.92
710.8628-2.7324-9.8183.85644.039613.20160.1325-0.0105-0.2969-0.2614-0.14610.35990.0615-0.3460.01350.1335-0.0493-0.07430.10570.01790.0822-20.386-31.881-25.181
81.78230.55050.61690.83820.96261.9865-0.0280.08950.0284-0.1163-0.00460.0948-0.0076-0.050.03250.0519-0.0112-0.04130.07940.00330.0349-17.32-21.778-30.35
93.8808-2.32072.28775.9238-0.88945.3525-0.27050.12010.1702-0.00310.12730.2314-0.66780.07560.14330.1067-0.0451-0.01810.0988-0.01170.067-17.393-6.76-20.785
103.24493.47750.50214.3085-0.11330.8540.0052-0.16470.37180.0817-0.03060.4983-0.1108-0.19890.02550.09010.051-0.01480.3816-0.04090.204-23.898-14.093-17.693
115.70011.5271-0.51592.08090.38085.13020.2324-0.45310.29450.1523-0.05040.1244-0.0634-0.077-0.18190.038-0.02460.01120.1118-0.01070.0307-12.085-24.257-12.057
123.2327-0.8879-0.49412.40580.23182.3039-0.1394-0.1202-0.32490.04620.081-0.39510.46040.29480.05850.14120.01110.00350.14520.01490.15543.832-36.189-11.887
132.56340.3069-2.692.5474-0.04784.9265-0.1989-0.515-0.4350.0068-0.0686-0.52560.59260.84030.26740.12180.08480.00270.23570.05760.189615.814-36.542-12.027
142.50480.66881.01211.76210.14165.21630.0089-0.0062-0.0869-0.12360.04450.1650.3847-0.4265-0.05350.05-0.0266-0.01590.08910.00850.0256-10.462-35.251-14.848
155.75251.206110.67260.28442.217919.81550.36380.141-0.22370.04370.09250.01970.71590.2226-0.45620.2786-0.0303-0.09790.2668-0.0060.2788-5.194-40.6734.515
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 - 151
5X-RAY DIFFRACTION5A152 - 188
6X-RAY DIFFRACTION6A189 - 228
7X-RAY DIFFRACTION7A229 - 244
8X-RAY DIFFRACTION8A245 - 289
9X-RAY DIFFRACTION9A290 - 319
10X-RAY DIFFRACTION10A320 - 341
11X-RAY DIFFRACTION11A342 - 357
12X-RAY DIFFRACTION12A358 - 418
13X-RAY DIFFRACTION13A419 - 452
14X-RAY DIFFRACTION14A453 - 477
15X-RAY DIFFRACTION15A478 - 488

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