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- PDB-3k8o: Crystal structure of human purine nucleoside phosphorylase in com... -

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Basic information

Entry
Database: PDB / ID: 3k8o
TitleCrystal structure of human purine nucleoside phosphorylase in complex with DATMe-ImmH
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / transition state analog inhibitor / DATMe-ImmH / hPNP / PNP / purine nucleoside phosphorylase / Cytoskeleton / Disease mutation / Glycosyltransferase
Function / homology
Function and homology information


nicotinamide riboside catabolic process / Defective PNP disrupts phosphorolysis of (deoxy)guanosine and (deoxy)inosine / purine-containing compound salvage / deoxyinosine catabolic process / purine nucleobase binding / inosine catabolic process / deoxyadenosine catabolic process / nucleotide biosynthetic process / dAMP catabolic process / urate biosynthetic process ...nicotinamide riboside catabolic process / Defective PNP disrupts phosphorolysis of (deoxy)guanosine and (deoxy)inosine / purine-containing compound salvage / deoxyinosine catabolic process / purine nucleobase binding / inosine catabolic process / deoxyadenosine catabolic process / nucleotide biosynthetic process / dAMP catabolic process / urate biosynthetic process / Ribavirin ADME / IMP catabolic process / nucleoside binding / guanosine phosphorylase activity / Purine catabolism / allantoin metabolic process / Purine salvage / purine-nucleoside phosphorylase / nucleobase-containing compound metabolic process / purine ribonucleoside salvage / purine-nucleoside phosphorylase activity / positive regulation of alpha-beta T cell differentiation / phosphate ion binding / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / secretory granule lumen / ficolin-1-rich granule lumen / response to xenobiotic stimulus / immune response / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Purine nucleoside phosphorylase I, inosine/guanosine-specific / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / Purine nucleoside phosphorylase / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-229 / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHo, M. / Rinaldo-matthis, A. / Almo, S.C. / Schramm, V.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Crystal structure of human purine nucleoside phosphorylase in complex with DATMe-Immucillin H
Authors: Ho, M. / Rinaldo-matthis, A. / Almo, S.C. / Schramm, V.L.
History
DepositionOct 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Purine nucleoside phosphorylase
Q: Purine nucleoside phosphorylase
S: Purine nucleoside phosphorylase
T: Purine nucleoside phosphorylase
U: Purine nucleoside phosphorylase
Y: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,25628
Polymers193,1096
Non-polymers3,14722
Water2,702150
1
E: Purine nucleoside phosphorylase
Q: Purine nucleoside phosphorylase
Y: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,12814
Polymers96,5553
Non-polymers1,57311
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11250 Å2
ΔGint-141 kcal/mol
Surface area29540 Å2
MethodPISA
2
S: Purine nucleoside phosphorylase
T: Purine nucleoside phosphorylase
U: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,12814
Polymers96,5553
Non-polymers1,57311
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11170 Å2
ΔGint-139 kcal/mol
Surface area29860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)269.212, 51.875, 129.069
Angle α, β, γ (deg.)90.00, 90.44, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Purine nucleoside phosphorylase / PNP / Inosine phosphorylase


Mass: 32184.877 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NP, PNP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P00491, purine-nucleoside phosphorylase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-229 / 7-({[(1R,2S)-2,3-DIHYDROXY-1-(HYDROXYMETHYL)PROPYL]AMINO}METHYL)-3,5-DIHYDRO-4H-PYRROLO[3,2-D]PYRIMIDIN-4-ONE


Mass: 268.269 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H16N4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 0.2 M Lithium sulfate, 25% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 70268 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.09 / Χ2: 0.982 / Net I/σ(I): 9.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.493.70.58869870.915199.7
2.49-2.583.70.49670010.952199.8
2.58-2.73.70.38269180.955199.9
2.7-2.843.70.26670000.9851100
2.84-3.023.70.1970211.0131100
3.02-3.253.70.12870221.063199.9
3.25-3.583.70.08670001.03199.8
3.58-4.093.40.07369240.981197.9
4.09-5.143.60.04971180.984199.8
5.14-203.60.04172770.943199.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0070refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 1 / SU B: 22.834 / SU ML: 0.246 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.615 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.272 3487 5.1 %RANDOM
Rwork0.223 ---
obs0.226 68897 97.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.11 Å2 / Biso mean: 46.589 Å2 / Biso min: 21.23 Å2
Baniso -1Baniso -2Baniso -3
1--4.33 Å20 Å2-1.28 Å2
2--7.23 Å20 Å2
3----2.92 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13288 0 194 150 13632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02213784
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.96918665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.38951693
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51223.439631
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.048152268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.49815102
X-RAY DIFFRACTIONr_chiral_restr0.10.22005
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110510
X-RAY DIFFRACTIONr_mcbond_it0.4761.58416
X-RAY DIFFRACTIONr_mcangle_it0.911213529
X-RAY DIFFRACTIONr_scbond_it1.54235368
X-RAY DIFFRACTIONr_scangle_it2.4094.55136
LS refinement shellResolution: 2.4→2.455 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 224 -
Rwork0.32 3640 -
all-3864 -
obs--75.32 %
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)
11.54240.89910.50560.91490.19371.64440.0102-0.15360.0778-0.0158-0.07350.19380.0037-0.55150.0633-0.02230.0103-0.0282-0.0472-0.0195-0.0085-48.536-3.015-13.908
21.7637-0.296-0.25780.9160.10981.35220.01040.26040.0611-0.1771-0.03760.0044-0.07560.04630.02730.0132-0.0068-0.025-0.2411-0.0055-0.0312-15.4373.408-29.443
32.6123-0.7999-0.56050.73390.16821.5704-0.0020.0984-0.1389-0.0249-0.01320.16560.159-0.14240.01510.0427-0.0278-0.0032-0.23150.0136-0.028517.22519.713-50.825
42.1714-0.17210.75891.30330.15892.1142-0.0648-0.32350.2470.2272-0.0434-0.193-0.07140.30130.10830.02950.0113-0.06-0.0392-0.02360.074650.28327.313-35.85
50.8160.1469-0.01641.1419-1.01812.91420.03490.27670.056-0.1932-0.2015-0.21990.20590.57670.16650.05290.05110.02880.01940.05240.038246.50525.371-72.916
61.21350.11970.19880.9809-0.61571.92530.032-0.21660.01050.0927-0.0326-0.0197-0.0632-0.11450.0007-0.04450.016-0.0246-0.2113-0.0321-0.07-18.5931.9917.467
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1E3 - 285
2X-RAY DIFFRACTION2Q2 - 285
3X-RAY DIFFRACTION3S3 - 285
4X-RAY DIFFRACTION4T3 - 284
5X-RAY DIFFRACTION5U3 - 287
6X-RAY DIFFRACTION6Y3 - 285

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