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- PDB-5k7y: Crystal structure of enzyme in purine metabolism -

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Basic information

Entry
Database: PDB / ID: 5k7y
TitleCrystal structure of enzyme in purine metabolism
ComponentsCytosolic purine 5'-nucleotidase
KeywordsHYDROLASE / enzyme / purine
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
Cytosolic purine 5'-nucleotidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 Å
AuthorsSkerlova, J. / Hnizda, A. / Pachl, P. / Rezacova, P.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science Foundation15-06582S Czech Republic
CitationJournal: Bmc Biol. / Year: 2016
Title: Oligomeric interface modulation causes misregulation of purine 5 -nucleotidase in relapsed leukemia.
Authors: Hnizda, A. / Skerlova, J. / Fabry, M. / Pachl, P. / Sinalova, M. / Vrzal, L. / Man, P. / Novak, P. / Rezacova, P. / Veverka, V.
History
DepositionMay 27, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,7058
Polymers64,0601
Non-polymers6457
Water6,125340
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)258,81832
Polymers256,2394
Non-polymers2,57928
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area20520 Å2
ΔGint-50 kcal/mol
Surface area75500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.519, 126.541, 130.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 64059.867 Da / Num. of mol.: 1 / Mutation: R367Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NT5C2, NT5B, NT5CP, PNT5 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P49902, 5'-nucleotidase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.94 Å3/Da / Density % sol: 58.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES/imidazol containing 200 mM NaCl, 30 % glycerol and 10 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.738→48.948 Å / Num. obs: 76477 / % possible obs: 98.2 % / Redundancy: 5.2 % / Biso Wilson estimate: 36.3 Å2 / Rrim(I) all: 0.053 / Net I/σ(I): 20.1
Reflection shellResolution: 1.738→1.747 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.9 / Rrim(I) all: 0.707 / % possible all: 89.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.417
Highest resolutionLowest resolution
Rotation48.95 Å3 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREP11.1.03phasing
REFMAC5.8.0131refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J2C

2j2c


Resolution: 1.79→48.33 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.278 / SU ML: 0.066 / SU R Cruickshank DPI: 0.0924 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.09
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1924 3555 5 %RANDOM
Rwork0.1706 ---
obs0.1717 67541 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 110.43 Å2 / Biso mean: 33.887 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0 Å2-0 Å2
2--0.48 Å2-0 Å2
3----0.14 Å2
Refinement stepCycle: final / Resolution: 1.79→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3843 0 42 344 4229
Biso mean--49.32 39.9 -
Num. residues----472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194189
X-RAY DIFFRACTIONr_bond_other_d0.0060.023968
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.9675683
X-RAY DIFFRACTIONr_angle_other_deg0.94339182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9065531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.07123.119202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71415746
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.881529
X-RAY DIFFRACTIONr_chiral_restr0.0930.2607
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024710
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021033
X-RAY DIFFRACTIONr_mcbond_it0.851.6221960
X-RAY DIFFRACTIONr_mcbond_other0.8421.6221959
X-RAY DIFFRACTIONr_mcangle_it1.3982.4282462
LS refinement shellResolution: 1.788→1.835 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 241 -
Rwork0.346 4594 -
all-4835 -
obs--92.54 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.76316.2388-0.77775.9958-0.98821.07370.0977-0.0589-0.5151-0.0441-0.0488-0.2630.22880.0042-0.04880.30810.0221-0.02380.3189-0.01530.3508-8.961-41.815-28.2
27.021-0.2421.19840.4468-1.19663.28990.18330.2439-0.6788-0.22530.03430.0940.6118-0.0545-0.21760.1818-0.0749-0.0530.195-0.01310.2619-12.206-38.724-13.633
31.73730.36570.06430.4622-0.12410.7724-0.03940.04270.0938-0.08540.0236-0.04760.02460.08260.01590.02060.00230.01710.0995-0.01210.029210.479-19.975-22.697
45.57530.24540.83175.7232-2.3686.5332-0.0048-0.4133-0.25590.3787-0.0425-0.16720.13630.27510.04720.1156-0.03370.00140.1782-0.01840.047919.131-20.279-5.785
54.49661.4360.73952.770.0722.2913-0.09450.18680.2913-0.06260.0078-0.2384-0.09640.18480.08680.02060.01340.00540.07430.02560.072119.425-14.443-21.701
64.84092.32462.58022.611.43382.178-0.21610.2030.4832-0.1410.03550.2052-0.1997-0.00010.18050.04370.01960.01830.14620.0290.10076.134-12.403-27.92
79.3581-1.8838-7.38182.63593.096810.56620.1867-0.0333-0.2281-0.256-0.10250.23820.1364-0.2784-0.08430.1339-0.0463-0.06510.11370.01150.0678-20.386-31.881-25.181
82.39540.50280.71281.46121.46032.87620.02370.05730.0244-0.07360.04960.0355-0.0115-0.0079-0.07320.0209-0.0135-0.02850.09070.00920.0482-17.32-21.778-30.35
93.0111-1.8871.99055.8176-2.07765.8206-0.10740.0540.15540.13190.07390.1502-0.58830.23290.03360.0925-0.0714-0.00180.1467-0.04850.1119-17.393-6.76-20.785
103.37292.9627-0.1734.0841-1.31464.3914-0.0311-0.30750.13320.19260.08880.5208-0.1461-0.6181-0.05770.08910.0490.01340.2709-0.01930.2598-23.898-14.093-17.693
119.3219-0.5563-2.56073.36440.43167.64640.2883-0.55520.72290.270.02890.0811-0.25720.0974-0.31710.075-0.02290.01460.1447-0.03010.0776-12.085-24.257-12.057
123.7742-1.13020.01552.4499-0.45022.3164-0.0361-0.2172-0.3247-0.0212-0.0067-0.39780.49780.26750.04290.1529-0.0075-0.01020.18410.03180.14873.832-36.189-11.887
133.30660.9032-1.94542.71610.19884.4624-0.1186-0.5435-0.68010.0097-0.063-0.67150.61880.81630.18160.12540.11120.02160.27670.0790.255315.814-36.542-12.027
143.72790.15081.24162.2506-0.52695.15550.0759-0.0301-0.1444-0.1980.04190.24340.4721-0.2795-0.11770.0787-0.0139-0.03160.09790.01120.0355-10.462-35.251-14.848
153.92741.27997.04970.50022.144713.33070.25330.148-0.15610.01950.03930.03010.64410.0469-0.29250.2341-0.0088-0.0790.2005-0.03910.2081-5.194-40.6734.515
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 27
2X-RAY DIFFRACTION2A28 - 47
3X-RAY DIFFRACTION3A48 - 127
4X-RAY DIFFRACTION4A128 - 151
5X-RAY DIFFRACTION5A152 - 188
6X-RAY DIFFRACTION6A189 - 228
7X-RAY DIFFRACTION7A229 - 244
8X-RAY DIFFRACTION8A245 - 289
9X-RAY DIFFRACTION9A290 - 319
10X-RAY DIFFRACTION10A320 - 341
11X-RAY DIFFRACTION11A342 - 357
12X-RAY DIFFRACTION12A358 - 418
13X-RAY DIFFRACTION13A419 - 452
14X-RAY DIFFRACTION14A453 - 477
15X-RAY DIFFRACTION15A478 - 488

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