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- PDB-5l4z: Crystal structure of enzyme in purine metabolism -

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Basic information

Entry
Database: PDB / ID: 5l4z
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 / 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
Cytosolic purine 5'-nucleotidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.84 Å
AuthorsHnizda, 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: PDBE / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,31514
Polymers64,1181
Non-polymers1,19713
Water3,783210
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)261,26156
Polymers256,4724
Non-polymers4,78952
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 area27170 Å2
ΔGint-43 kcal/mol
Surface area73760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.323, 126.503, 130.515
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: 64117.945 Da / Num. of mol.: 1 / Mutation: R238W
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


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 58.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM MOPS/HEPES-Na containing 100 mM NaCl, 15 % 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: Sep 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.839→48.305 Å / Num. obs: 65417 / % possible obs: 99.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 35.6 Å2 / Rrim(I) all: 0.055 / Net I/σ(I): 18.5
Reflection shellResolution: 1.839→1.849 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2 / Rrim(I) all: 0.71 / % possible all: 99.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.438
Highest resolutionLowest resolution
Rotation45.42 Å2.11 Å

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Processing

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

2j2c


Resolution: 1.84→45.42 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU R Cruickshank DPI: 0.0994 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.099
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2049 2101 3.2 %RANDOM
Rwork0.1768 ---
obs0.1777 63308 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 119.99 Å2 / Biso mean: 38.287 Å2 / Biso min: 14.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.84→45.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3834 0 78 211 4123
Biso mean--59.37 37.46 -
Num. residues----470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194123
X-RAY DIFFRACTIONr_bond_other_d00.023891
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.9685574
X-RAY DIFFRACTIONr_angle_other_deg3.56238984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2775505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72423.198197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.23915712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.571526
X-RAY DIFFRACTIONr_chiral_restr0.0970.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024581
X-RAY DIFFRACTIONr_gen_planes_other0.0140.021009
X-RAY DIFFRACTIONr_mcbond_it1.00721919
X-RAY DIFFRACTIONr_mcbond_other0.9951.9991918
X-RAY DIFFRACTIONr_mcangle_it1.6012.9942406
LS refinement shellResolution: 1.839→1.887 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 153 -
Rwork0.337 4593 -
all-4746 -
obs--98.26 %
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)
113.627510.4985-2.223210.23770.88573.689-0.29230.0518-0.8250.10220.0846-0.31110.522-0.06880.20780.5267-0.0119-0.01020.40150.08480.6965-4.645-37.717-31.15
216.608417.26847.701819.08355.228210.8982-0.17260.6157-1.5226-0.74730.7481-1.41681.2526-0.0758-0.57560.63630.047-0.09530.4799-0.22020.7919-11.494-46.87-22.854
31.80470.40540.21670.6346-0.07550.8-0.02330.06360.0483-0.10170.02-0.0070.08090.0350.00340.02870.00180.01160.0394-0.0140.02516.069-22.23-20.757
41.7362.0030.12992.9958-1.33378.33740.0486-0.1009-0.15980.1621-0.1453-0.16090.13360.43170.09680.08570.01370.01250.1371-0.00060.062219.544-20.751-6.537
54.94882.19120.56243.65510.00092.1499-0.08980.35850.333-0.04970.062-0.2603-0.15170.1770.02770.04150.00810.01380.0710.03580.101419.965-13.293-21.463
64.74242.37242.43862.3381.61362.0668-0.22930.23270.4241-0.16130.05360.2033-0.1382-0.03760.17570.04180.00460.00870.12660.04320.09734.932-12.903-28.318
71.44590.35730.49331.79590.82062.96590.01680.0071-0.0382-0.0260.00070.02140.0995-0.0045-0.01750.0311-0.0187-0.03330.0704-0.00550.0541-16.958-23.212-27.474
82.734-0.18871.30585.5858-0.72196.1711-0.14850.11230.0605-0.10920.04050.4939-0.3975-0.08850.10810.0941-0.0111-0.03690.0657-0.03730.1468-21.537-7.411-22.502
94.4169-0.3733-1.22911.71110.21862.4577-0.0276-0.12240.0627-0.00670.0242-0.0928-0.0018-0.00960.00350.048-0.0389-0.01630.08650.01040.0211-9.006-26.262-13.186
1013.0447-0.84757.43621.0066-2.470611.87990.3543-0.0921-0.12130.0382-0.1624-0.1990.96980.7528-0.19180.61130.17910.05270.39850.06830.833218.334-46.455-7.262
114.14450.98240.02081.8755-0.19691.94350.0716-0.1869-0.3884-0.1439-0.0602-0.22290.25610.1372-0.01130.10010.02910.00870.04330.01520.0572.386-35.205-13.831
124.18530.09786.82730.2335-0.238711.82870.43820.1386-0.2438-0.03680.0430.04330.81170.1806-0.48120.2031-0.0026-0.05020.1614-0.02150.2163-5.125-40.7224.824
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 19
2X-RAY DIFFRACTION2A20 - 34
3X-RAY DIFFRACTION3A35 - 125
4X-RAY DIFFRACTION4A126 - 151
5X-RAY DIFFRACTION5A152 - 191
6X-RAY DIFFRACTION6A192 - 227
7X-RAY DIFFRACTION7A228 - 297
8X-RAY DIFFRACTION8A298 - 333
9X-RAY DIFFRACTION9A334 - 383
10X-RAY DIFFRACTION10A384 - 422
11X-RAY DIFFRACTION11A423 - 477
12X-RAY DIFFRACTION12A478 - 488

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