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- PDB-6ddl: Crystal structure of the single mutant (D52N) of NT5C2-Q523X in t... -

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Basic information

Entry
Database: PDB / ID: 6ddl
TitleCrystal structure of the single mutant (D52N) of NT5C2-Q523X in the basal state
ComponentsCytosolic purine 5'-nucleotidase
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


nucleoside phosphotransferase / GMP catabolic process to guanine / nucleoside phosphotransferase activity / GMP metabolic process / : / Abacavir metabolism / dGMP metabolic process / negative regulation of defense response to virus by host / adenosine metabolic process / amide catabolic process ...nucleoside phosphotransferase / GMP catabolic process to guanine / nucleoside phosphotransferase activity / GMP metabolic process / : / Abacavir metabolism / dGMP metabolic process / negative regulation of defense response to virus by host / adenosine metabolic process / amide catabolic process / : / dGMP catabolic process / IMP-specific 5'-nucleotidase / : / IMP catabolic process / Ribavirin ADME / IMP metabolic process / Purine catabolism / 5'-nucleotidase / allantoin metabolic process / 5'-nucleotidase activity / protein K48-linked ubiquitination / ubiquitin protein ligase activity / ATP binding / metal ion binding / identical protein 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
PHOSPHATE ION / Cytosolic purine 5'-nucleotidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 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)125,3906
Polymers125,0102
Non-polymers3804
Water11,782654
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)250,78012
Polymers250,0204
Non-polymers7608
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area26140 Å2
ΔGint-166 kcal/mol
Surface area76450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.446, 123.634, 91.251
Angle α, β, γ (deg.)90.00, 115.51, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-821-

HOH

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Components

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


Mass: 62505.035 Da / Num. of mol.: 2 / Fragment: residues 1-523 / Mutation: 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


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 654 / 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: 2.93 Å3/Da / Density % sol: 57.16 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 4.6
Details: sodium acetate trihydrate (pH 4.6) and 30% (v/v) 2-Methyl-2, 4-pentanediol (MPD), 20 mM calcium chloride dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.26→49.44 Å / Num. obs: 67088 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 34.4 Å2 / CC1/2: 0.95 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.05 / Rrim(I) all: 0.13 / Χ2: 1.72 / Net I/σ(I): 21.4
Reflection shellResolution: 2.26→2.31 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.2 / CC1/2: 0.96 / Rpim(I) all: 0.2 / Rrim(I) all: 0.54 / Χ2: 0.61

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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: 6DDC

6ddc


Resolution: 2.26→49.438 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.54
RfactorNum. reflection% reflection
Rfree0.2432 6781 10.11 %
Rwork0.194 --
obs0.1991 67088 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.26→49.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7618 0 20 675 8313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077828
X-RAY DIFFRACTIONf_angle_d0.88710570
X-RAY DIFFRACTIONf_dihedral_angle_d19.2734624
X-RAY DIFFRACTIONf_chiral_restr0.051129
X-RAY DIFFRACTIONf_plane_restr0.0051337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.28570.28132240.21892004X-RAY DIFFRACTION100
2.2857-2.31260.28162140.21622016X-RAY DIFFRACTION100
2.3126-2.34080.2812190.21181996X-RAY DIFFRACTION100
2.3408-2.37040.28542240.21362011X-RAY DIFFRACTION100
2.3704-2.40160.28822270.20612012X-RAY DIFFRACTION100
2.4016-2.43450.27212270.20941969X-RAY DIFFRACTION100
2.4345-2.46930.29182140.19352014X-RAY DIFFRACTION100
2.4693-2.50610.25662100.19622058X-RAY DIFFRACTION100
2.5061-2.54530.26282320.19241957X-RAY DIFFRACTION100
2.5453-2.5870.25172110.19262011X-RAY DIFFRACTION100
2.587-2.63160.26972160.19492052X-RAY DIFFRACTION100
2.6316-2.67950.25662320.18881970X-RAY DIFFRACTION100
2.6795-2.7310.26472230.18971981X-RAY DIFFRACTION100
2.731-2.78680.2792360.22048X-RAY DIFFRACTION100
2.7868-2.84740.27142480.19761971X-RAY DIFFRACTION100
2.8474-2.91360.25372370.20081993X-RAY DIFFRACTION100
2.9136-2.98640.23792210.19742007X-RAY DIFFRACTION100
2.9864-3.06720.29272210.21472021X-RAY DIFFRACTION100
3.0672-3.15740.24472290.21532045X-RAY DIFFRACTION100
3.1574-3.25930.25662240.20082004X-RAY DIFFRACTION100
3.2593-3.37580.23612120.19452013X-RAY DIFFRACTION100
3.3758-3.51090.22862450.19641990X-RAY DIFFRACTION100
3.5109-3.67060.23132260.18321996X-RAY DIFFRACTION100
3.6706-3.86410.22942150.18252030X-RAY DIFFRACTION100
3.8641-4.10610.22672440.18291999X-RAY DIFFRACTION100
4.1061-4.42290.20832350.16632012X-RAY DIFFRACTION100
4.4229-4.86770.2042490.16032000X-RAY DIFFRACTION100
4.8677-5.57120.23731920.1882061X-RAY DIFFRACTION100
5.5712-7.01590.25722390.21642029X-RAY DIFFRACTION100
7.0159-49.450.23292350.21942037X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 34.081 Å / Origin y: 19.8855 Å / Origin z: 24.4505 Å
111213212223313233
T0.1986 Å2-0.0036 Å20.0123 Å2-0.1943 Å20.0015 Å2--0.1805 Å2
L0.121 °20.0015 °20.0661 °2-0.2591 °20.0885 °2--0.0349 °2
S-0.0036 Å °0.0055 Å °-0.0077 Å °-0.0195 Å °0.0202 Å °-0.014 Å °-0.0038 Å °-0.006 Å °0 Å °
Refinement TLS groupSelection details: all

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