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- PDB-6de3: Crystal structure of the double mutant (R39Q/D52N) of the full-le... -

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Basic information

Entry
Database: PDB / ID: 6de3
TitleCrystal structure of the double mutant (R39Q/D52N) of the full-length NT5C2 in the active state
ComponentsCytosolic purine 5'-nucleotidase
KeywordsHYDROLASE
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
ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / Cytosolic purine 5'-nucleotidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 Å
AuthorsForouhar, F. / Dieck, C.L. / Tzoneva, G. / Carpenter, Z. / Ambesi-Impiombato, A. / Sanchez-Martin, M. / Kirschner-Schwabe, R. / Lew, S. / Seetharaman, J. / Ferrando, A.A. / Tong, L.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA206501 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA013696 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10OD012018 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)T32-CA09503 United States
CitationJournal: Cancer Cell / Year: 2018
Title: Structure and Mechanisms of NT5C2 Mutations Driving Thiopurine Resistance in Relapsed Lymphoblastic Leukemia.
Authors: Dieck, C.L. / Tzoneva, G. / Forouhar, F. / Carpenter, Z. / Ambesi-Impiombato, A. / Sanchez-Martin, M. / Kirschner-Schwabe, R. / Lew, S. / Seetharaman, J. / Tong, L. / Ferrando, A.A.
History
DepositionMay 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,5534
Polymers66,9271
Non-polymers6263
Water90150
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)270,21316
Polymers267,7074
Non-polymers2,50612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area12660 Å2
ΔGint-74 kcal/mol
Surface area77800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.362, 129.098, 131.016
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-603-

MG

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Components

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


Mass: 66926.672 Da / Num. of mol.: 1 / Mutation: R39Q, D52N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NT5C2, NT5B, NT5CP, PNT5 / Plasmid: pLOC_NT5C2 / Cell (production host): Rosetta 2(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P49902, 5'-nucleotidase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#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 / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5
Details: 100 mM HEPES (pH 7.5), 12% (w/v) PEG 3350, 5 mM ATP, 5 mM IMP, and 5 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: SBC-2 / Detector: CCD / Date: Oct 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.06→46.181 Å / Num. obs: 14798 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 50.18 Å2 / CC1/2: 0.96 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.07 / Rrim(I) all: 0.15 / Χ2: 0.96 / Net I/av σ(I): 9.8 / Net I/σ(I): 9.8
Reflection shellResolution: 3.06→3.12 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 872 / CC1/2: 0.86 / Rpim(I) all: 0.25 / Rrim(I) all: 0.56 / Χ2: 0.84 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data reduction
HKL-2000data scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DDH

6ddh


Resolution: 3.06→46.181 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.39
RfactorNum. reflection% reflection
Rfree0.2263 1488 10.06 %
Rwork0.1672 --
obs0.1732 14798 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.06→46.181 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3851 0 37 50 3938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083987
X-RAY DIFFRACTIONf_angle_d0.9885392
X-RAY DIFFRACTIONf_dihedral_angle_d15.4392351
X-RAY DIFFRACTIONf_chiral_restr0.052574
X-RAY DIFFRACTIONf_plane_restr0.006677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0602-3.15890.34851250.23821077X-RAY DIFFRACTION89
3.1589-3.27180.32081310.22631193X-RAY DIFFRACTION97
3.2718-3.40280.31451320.21651219X-RAY DIFFRACTION99
3.4028-3.55760.26091430.19751209X-RAY DIFFRACTION100
3.5576-3.7450.23581520.17141187X-RAY DIFFRACTION99
3.745-3.97960.20211270.14381238X-RAY DIFFRACTION99
3.9796-4.28660.19631470.14121215X-RAY DIFFRACTION99
4.2866-4.71760.20071220.12061234X-RAY DIFFRACTION99
4.7176-5.39940.18671330.11911237X-RAY DIFFRACTION99
5.3994-6.79920.19121320.17871238X-RAY DIFFRACTION98
6.7992-46.18620.20641440.18641263X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -0.1124 Å / Origin y: 39.3518 Å / Origin z: 19.2402 Å
111213212223313233
T-0.085 Å20.1236 Å2-0.035 Å2--0.1288 Å20.0602 Å2---0.0032 Å2
L0.4822 °2-0.0164 °2-0.0514 °2-0.2117 °20.0385 °2--0.4404 °2
S-0.01 Å °-0.0768 Å °-0.1525 Å °0.1483 Å °-0.0866 Å °0.0524 Å °0.4334 Å °-0.1952 Å °-0.3189 Å °
Refinement TLS groupSelection details: all

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