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- PDB-5l50: Crystal structure of enzyme in purine metabolism -

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Basic information

Entry
Database: PDB / ID: 5l50
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: 1.643 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)65,22813
Polymers64,1231
Non-polymers1,10512
Water4,594255
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)260,91252
Polymers256,4924
Non-polymers4,42148
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 area25830 Å2
ΔGint-54 kcal/mol
Surface area74320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.356, 125.988, 130.781
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: 64122.945 Da / Num. of mol.: 1 / Mutation: L375F
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.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 58.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 200 mM MES/imidazol (pH 6.5) containing 100 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: Sep 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.643→48.989 Å / Num. obs: 90521 / % possible obs: 98.6 % / Redundancy: 4.4 % / Rrim(I) all: 0.064 / Net I/σ(I): 14.3
Reflection shellResolution: 1.643→1.651 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.9 / Rrim(I) all: 0.669 / % possible all: 95.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.446
Highest resolutionLowest resolution
Rotation48.99 Å1.94 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: 1.643→48.989 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU R Cruickshank DPI: 0.0719 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.072
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1956 2100 2.3 %RANDOM
Rwork0.1753 ---
obs0.1758 88417 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 87.83 Å2 / Biso mean: 29.463 Å2 / Biso min: 9 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.643→48.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3848 0 72 262 4182
Biso mean--50.57 33.57 -
Num. residues----472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194175
X-RAY DIFFRACTIONr_bond_other_d00.023945
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.9685648
X-RAY DIFFRACTIONr_angle_other_deg3.56139108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8945514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.08822.836201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60515726
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5571531
X-RAY DIFFRACTIONr_chiral_restr0.0980.2605
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024658
X-RAY DIFFRACTIONr_gen_planes_other0.0160.021035
X-RAY DIFFRACTIONr_mcbond_it0.8621.4821944
X-RAY DIFFRACTIONr_mcbond_other0.8571.4811943
X-RAY DIFFRACTIONr_mcangle_it1.4172.2192440
LS refinement shellResolution: 1.643→1.685 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 139 -
Rwork0.362 5868 -
all-6007 -
obs--89.5 %
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)
19.1623-6.1075-0.87594.49820.86480.28270.0165-0.0862-0.64680.1640.00850.34110.1571-0.0373-0.0250.3147-0.0029-0.0130.29540.03540.2485.305-38.02931.014
217.1275-5.9761-2.872214.82774.054613.93480.09550.7625-0.3756-0.0126-0.09750.20050.45610.48950.00210.27970.0002-0.07050.25890.00710.225315.631-48.70523.601
36.31610.03610.89790.63441.23472.82980.025-0.3392-0.69670.17070.0648-0.12190.43370.0559-0.08980.17870.07740.04530.17440.04180.286812.2-39.00813.818
41.419-0.54870.05980.51380.0430.7495-0.05-0.08560.0740.08410.02280.01830.0055-0.08910.02720.0265-0.00690.01160.10380.00080.0148-10.709-19.98522.517
52.0471-0.6861.66831.5390.77645.06820.06380.15320.0469-0.1746-0.09430.05810.0366-0.08650.03040.0612-0.01880.0180.11460.00360.0381-14.907-20.0829.883
62.5911-0.77811.04732.8802-0.42331.3207-0.1155-0.14590.35890.03910.03150.2024-0.1908-0.12790.08390.05240.00430.00820.1389-0.03220.0994-20.011-9.71721.541
74.1509-0.98851.215610.9408-3.0372.8322-0.1962-0.33840.47070.34020.0846-0.0105-0.1603-0.03370.11170.0480.0155-0.02550.1775-0.05150.0671.221-15.4935.522
81.3566-0.00750.24271.2283-0.46561.87530.00540.0174-0.0256-0.00680.0032-0.02110.12170.0537-0.00860.04280.0207-0.02870.12670.00560.027116.674-23.24727.581
92.10070.47331.00735.63530.59514.9702-0.0908-0.08190.01680.10510.0429-0.4519-0.30460.12690.04790.07860.0138-0.02160.13010.02740.116621.655-7.54622.109
102.470.5374-0.17471.5928-0.07561.6779-0.01310.124-0.122-0.04550.00860.18850.1964-0.08340.00460.0710.0246-0.0110.1192-0.01020.03811.531-32.28811.44
112.6824-0.7456-0.39011.25840.18181.8279-0.01060.1695-0.28730.0813-0.02370.15170.247-0.15450.03440.0815-0.02810.01020.0708-0.01310.0368-4.357-36.04913.362
123.7784-0.93896.66970.5065-1.477611.89620.2866-0.1337-0.1855-0.04920.0772-0.02710.5307-0.2225-0.36380.1980.0034-0.06330.18330.02680.16975.195-40.78-4.592
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 20
2X-RAY DIFFRACTION2A21 - 27
3X-RAY DIFFRACTION3A28 - 47
4X-RAY DIFFRACTION4A48 - 128
5X-RAY DIFFRACTION5A129 - 162
6X-RAY DIFFRACTION6A163 - 209
7X-RAY DIFFRACTION7A210 - 225
8X-RAY DIFFRACTION8A226 - 297
9X-RAY DIFFRACTION9A298 - 334
10X-RAY DIFFRACTION10A335 - 418
11X-RAY DIFFRACTION11A419 - 477
12X-RAY DIFFRACTION12A478 - 488

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