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- PDB-6ddb: Crystal structure of the double mutant (D52N/R367Q) of NT5C2-537X... -

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Basic information

Entry
Database: PDB / ID: 6ddb
TitleCrystal structure of the double mutant (D52N/R367Q) 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 / 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
: / PHOSPHATE ION / Cytosolic purine 5'-nucleotidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 / 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.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.value / _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)128,3458
Polymers127,8552
Non-polymers4906
Water3,117173
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)256,69016
Polymers255,7114
Non-polymers98012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area23230 Å2
ΔGint-163 kcal/mol
Surface area75110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.126, 123.123, 90.314
Angle α, β, γ (deg.)90.00, 115.50, 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: 63927.688 Da / Num. of mol.: 2 / Fragment: residues 1-536 / 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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 173 / 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: 3.3 Å3/Da / Density % sol: 61.5 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 4.6
Details: 100 mM sodium acetate trihydrate, 30% (v/v) 2-Methyl-2, 4-pentanediol, 20 mM calcium chloride dihydrate, and 5 mM MnCl2

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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: May 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→49.125 Å / Num. obs: 38433 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 42 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.04 / Rrim(I) all: 0.09 / Χ2: 1.7 / Net I/av σ(I): 24.6 / Net I/σ(I): 24.4
Reflection shellResolution: 2.8→2.91 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 5.7 / Num. unique obs: 3812 / CC1/2: 0.93 / Rpim(I) all: 0.17 / Rrim(I) all: 0.42 / Χ2: 1.6 / % possible all: 98.2

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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: 2XCW

2xcw


Resolution: 2.8→49.125 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.49
RfactorNum. reflection% reflection
Rfree0.2914 3450 10.03 %
Rwork0.2171 --
obs0.2251 34390 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→49.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7624 0 22 173 7819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087840
X-RAY DIFFRACTIONf_angle_d1.00210594
X-RAY DIFFRACTIONf_dihedral_angle_d18.7684626
X-RAY DIFFRACTIONf_chiral_restr0.0511128
X-RAY DIFFRACTIONf_plane_restr0.0061342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.83840.37531500.25981220X-RAY DIFFRACTION98
2.8384-2.87890.37131500.23011229X-RAY DIFFRACTION98
2.8789-2.92190.3061200.20861219X-RAY DIFFRACTION98
2.9219-2.96750.33831190.20481252X-RAY DIFFRACTION98
2.9675-3.01620.36691440.22281215X-RAY DIFFRACTION98
3.0162-3.06820.34661390.22481245X-RAY DIFFRACTION98
3.0682-3.1240.32631330.22891221X-RAY DIFFRACTION99
3.124-3.1840.31751200.21621221X-RAY DIFFRACTION98
3.184-3.2490.32321370.22191274X-RAY DIFFRACTION99
3.249-3.31960.3051420.19921207X-RAY DIFFRACTION98
3.3196-3.39680.31381460.21031219X-RAY DIFFRACTION98
3.3968-3.48180.29071390.19961245X-RAY DIFFRACTION99
3.4818-3.57590.29311240.1981242X-RAY DIFFRACTION99
3.5759-3.68110.261380.19581217X-RAY DIFFRACTION99
3.6811-3.79980.26171460.17271239X-RAY DIFFRACTION99
3.7998-3.93560.27111310.19181252X-RAY DIFFRACTION99
3.9356-4.09310.26621540.19361221X-RAY DIFFRACTION99
4.0931-4.27930.26321250.18951254X-RAY DIFFRACTION99
4.2793-4.50480.26021360.19171251X-RAY DIFFRACTION99
4.5048-4.78680.26831440.19641226X-RAY DIFFRACTION99
4.7868-5.1560.26481650.19941220X-RAY DIFFRACTION99
5.156-5.67420.32831320.23041266X-RAY DIFFRACTION99
5.6742-6.49360.31181530.25651239X-RAY DIFFRACTION99
6.4936-8.17520.30381380.25691268X-RAY DIFFRACTION99
8.1752-49.13290.3121250.30661278X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 34.8416 Å / Origin y: 19.6615 Å / Origin z: 24.5658 Å
111213212223313233
T0.0433 Å2-0.0013 Å20.0133 Å2-0.0533 Å20.0001 Å2--0.0386 Å2
L0.174 °20.0894 °20.0854 °2-0.1075 °2-0.0316 °2--0.1297 °2
S-0.008 Å °0.0225 Å °-0.0156 Å °-0.0093 Å °0.0231 Å °-0.0221 Å °-0.0026 Å °-0.0499 Å °0.0361 Å °
Refinement TLS groupSelection details: all

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