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- PDB-6ddc: Crystal structure of the single mutant (D52N) of NT5C2-537X in th... -

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Basic information

Entry
Database: PDB / ID: 6ddc
TitleCrystal structure of the single mutant (D52N) of NT5C2-537X in the basal state, Northeast Structural Genomics Consortium Target
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 / dGMP catabolic process / adenosine metabolic 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 / dGMP catabolic process / adenosine metabolic process / : / amide 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: 2.91 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. ...Forouhar, 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. / Northeast Structural Genomics Consortium (NESG)
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 9, 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 ...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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _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

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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)128,3428
Polymers127,9142
Non-polymers4286
Water4,954275
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)256,68416
Polymers255,8274
Non-polymers85712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area25370 Å2
ΔGint-218 kcal/mol
Surface area77530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.555, 124.151, 90.736
Angle α, β, γ (deg.)90.00, 116.25, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 63956.750 Da / Num. of mol.: 2 / Fragment: residues 1-536 / 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 275 / 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: 3.2 Å3/Da / Density % sol: 61.5 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 4.6
Details: 100 mM sodium acetate trihydrate (pH 4.6) and 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.91→39.424 Å / Num. obs: 30412 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 43.8 Å2 / CC1/2: 0.94 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.07 / Rrim(I) all: 0.12 / Χ2: 0.87 / Net I/av σ(I): 8.9 / Net I/σ(I): 8.9
Reflection shellResolution: 2.91→3.03 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3328 / CC1/2: 0.8 / Rpim(I) all: 0.32 / Rrim(I) all: 0.58 / Χ2: 0.57 / % possible all: 96.5

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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: 2.91→39.424 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.43
RfactorNum. reflection% reflection
Rfree0.2643 3064 10.07 %
Rwork0.181 --
obs0.1873 30412 96.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.91→39.424 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7741 0 22 276 8039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087957
X-RAY DIFFRACTIONf_angle_d0.96710747
X-RAY DIFFRACTIONf_dihedral_angle_d19.9454706
X-RAY DIFFRACTIONf_chiral_restr0.0521148
X-RAY DIFFRACTIONf_plane_restr0.0061358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.91-2.95550.36421450.25261227X-RAY DIFFRACTION96
2.9555-3.00390.39271400.24831225X-RAY DIFFRACTION97
3.0039-3.05570.39171450.25751244X-RAY DIFFRACTION97
3.0557-3.11130.38051160.23581258X-RAY DIFFRACTION97
3.1113-3.17110.36511430.22621296X-RAY DIFFRACTION98
3.1711-3.23580.36741340.22281243X-RAY DIFFRACTION98
3.2358-3.30610.33291460.20431237X-RAY DIFFRACTION98
3.3061-3.3830.29911620.20581227X-RAY DIFFRACTION98
3.383-3.46750.28921420.19321255X-RAY DIFFRACTION97
3.4675-3.56120.31581370.17591253X-RAY DIFFRACTION97
3.5612-3.66590.26211370.17451269X-RAY DIFFRACTION97
3.6659-3.78420.24971490.16051239X-RAY DIFFRACTION97
3.7842-3.91930.25511340.15781229X-RAY DIFFRACTION97
3.9193-4.07610.25711480.16291248X-RAY DIFFRACTION97
4.0761-4.26140.20511350.14751260X-RAY DIFFRACTION97
4.2614-4.48570.19941390.13381238X-RAY DIFFRACTION96
4.4857-4.76630.23071320.13131249X-RAY DIFFRACTION96
4.7663-5.13360.23361360.14051242X-RAY DIFFRACTION96
5.1336-5.64890.27171310.16681256X-RAY DIFFRACTION96
5.6489-6.46320.28121360.18131219X-RAY DIFFRACTION95
6.4632-8.13120.23681360.18661224X-RAY DIFFRACTION94
8.1312-39.42750.22671410.19451210X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: 34.6127 Å / Origin y: 19.5647 Å / Origin z: 24.5928 Å
111213212223313233
T0.0857 Å2-0.0004 Å20.0042 Å2-0.1006 Å2-0.0053 Å2--0.0936 Å2
L0.0287 °20.0387 °20.0374 °2-0.1437 °20.0246 °2--0.0603 °2
S-0.012 Å °-0.0024 Å °-0.0057 Å °0.0033 Å °0.0217 Å °-0.0233 Å °0.0071 Å °-0.007 Å °0 Å °
Refinement TLS groupSelection details: all

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