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- PDB-6ddk: Crystal structure of the double mutant (D52N/R367Q) of the full-l... -

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Basic information

Entry
Database: PDB / ID: 6ddk
TitleCrystal structure of the double mutant (D52N/R367Q) of the full-length NT5C2 in the basal 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 / 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
PHOSPHATE ION / Cytosolic purine 5'-nucleotidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 Center for Research Resources (NIH/NCRR)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 10, 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
B: Cytosolic purine 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,0434
Polymers133,8532
Non-polymers1902
Water9,260514
1
A: Cytosolic purine 5'-nucleotidase
B: Cytosolic purine 5'-nucleotidase
hetero molecules

A: Cytosolic purine 5'-nucleotidase
B: Cytosolic purine 5'-nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,0878
Polymers267,7074
Non-polymers3804
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area32340 Å2
ΔGint-178 kcal/mol
Surface area76860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.852, 171.396, 122.424
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-921-

HOH

21B-857-

HOH

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Components

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


Mass: 66926.672 Da / Num. of mol.: 2 / Mutation: D52N, R367Q
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


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / 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: 2.4 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5
Details: 100 mM HEPES (pH 7.5), 10% (w/v) PEG 3350, and 200 mM L-proline

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 6, 2015
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→49.81 Å / Num. obs: 44612 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.5 % / Biso Wilson estimate: 30.9 Å2 / CC1/2: 0.97 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.039 / Rrim(I) all: 0.135 / Χ2: 1 / Net I/av σ(I): 20.4 / Net I/σ(I): 20.4
Reflection shellResolution: 2.5→2.55 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 2734 / CC1/2: 0.93 / Rpim(I) all: 0.15 / Rrim(I) all: 0.55 / Χ2: 0.68 / % possible all: 100

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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: 6DDB

6ddb


Resolution: 2.5→49.81 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.13
RfactorNum. reflection% reflection
Rfree0.2227 4459 10 %
Rwork0.1623 --
obs0.1684 44612 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→49.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8002 0 10 516 8528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078217
X-RAY DIFFRACTIONf_angle_d0.90611102
X-RAY DIFFRACTIONf_dihedral_angle_d19.7754869
X-RAY DIFFRACTIONf_chiral_restr0.051188
X-RAY DIFFRACTIONf_plane_restr0.0051410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.52850.2841560.19221311X-RAY DIFFRACTION100
2.5285-2.55820.2451560.18831336X-RAY DIFFRACTION100
2.5582-2.58940.27491400.18031323X-RAY DIFFRACTION100
2.5894-2.62220.24431570.17551310X-RAY DIFFRACTION100
2.6222-2.65670.30331300.17761331X-RAY DIFFRACTION100
2.6567-2.69310.32181490.20021344X-RAY DIFFRACTION100
2.6931-2.73150.25561550.19441288X-RAY DIFFRACTION100
2.7315-2.77230.28671420.19321348X-RAY DIFFRACTION100
2.7723-2.81560.28571550.18241291X-RAY DIFFRACTION100
2.8156-2.86180.26861600.18171310X-RAY DIFFRACTION100
2.8618-2.91110.24781420.17311341X-RAY DIFFRACTION100
2.9111-2.9640.23441370.16991336X-RAY DIFFRACTION100
2.964-3.0210.29721340.18381336X-RAY DIFFRACTION100
3.021-3.08270.26781460.19161349X-RAY DIFFRACTION100
3.0827-3.14970.27471530.18821312X-RAY DIFFRACTION100
3.1497-3.2230.27411480.19871339X-RAY DIFFRACTION100
3.223-3.30360.25311610.19981324X-RAY DIFFRACTION100
3.3036-3.39290.24831460.17741337X-RAY DIFFRACTION100
3.3929-3.49270.2121690.16171307X-RAY DIFFRACTION100
3.4927-3.60540.22351540.15281330X-RAY DIFFRACTION100
3.6054-3.73420.18691300.14781352X-RAY DIFFRACTION100
3.7342-3.88370.16841440.13571339X-RAY DIFFRACTION100
3.8837-4.06030.20651580.1351340X-RAY DIFFRACTION100
4.0603-4.27430.16531490.13271336X-RAY DIFFRACTION100
4.2743-4.54190.18761410.12811364X-RAY DIFFRACTION100
4.5419-4.89230.19171590.12461344X-RAY DIFFRACTION100
4.8923-5.38410.1831460.13891358X-RAY DIFFRACTION100
5.3841-6.1620.20141520.16111372X-RAY DIFFRACTION100
6.162-7.75870.19391470.16881381X-RAY DIFFRACTION100
7.7587-49.82040.18061430.16881464X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 16.061 Å / Origin y: 56.3292 Å / Origin z: 27.8422 Å
111213212223313233
T0.0432 Å2-0.0078 Å20.0029 Å2-0.0523 Å20.0011 Å2--0.0433 Å2
L0.0493 °2-0.0115 °2-0.0172 °2-0.0732 °2-0.0067 °2--0.0832 °2
S0.0257 Å °0.0005 Å °-0.0158 Å °-0.0202 Å °-0.0463 Å °-0.0461 Å °-0.0395 Å °0.034 Å °-0.0247 Å °
Refinement TLS groupSelection details: all

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