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- PDB-8sws: Structure of K. lactis PNP S42E-H98R variant bound to transition ... -

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Basic information

Entry
Database: PDB / ID: 8sws
TitleStructure of K. lactis PNP S42E-H98R variant bound to transition state analog DADMe-IMMUCILLIN G and sulfate
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / PENTOSYLTRANSFERASE / PURINE NUCLEOSIDE PHOSPHORYLASE
Function / homology
Function and homology information


nucleoside metabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / cytoplasm
Similarity search - Function
Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / Purine nucleoside phosphorylase / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily
Similarity search - Domain/homology
Chem-IM5 / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesKluyveromyces lactis NRRL Y-1140 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsFedorov, E. / Ghosh, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM041916 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA013330 United States
CitationJournal: Biochemistry / Year: 2023
Title: Phosphate Binding in PNP Alters Transition-State Analogue Affinity and Subunit Cooperativity.
Authors: Minnow, Y.V.T. / Schramm, V.L. / Almo, S.C. / Ghosh, A.
History
DepositionMay 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 14, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.source_name / _pdbx_initial_refinement_model.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase
B: Purine nucleoside phosphorylase
C: Purine nucleoside phosphorylase
D: Purine nucleoside phosphorylase
E: Purine nucleoside phosphorylase
F: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,41520
Polymers201,3376
Non-polymers2,07814
Water5,639313
1
A: Purine nucleoside phosphorylase
B: Purine nucleoside phosphorylase
C: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,6129
Polymers100,6693
Non-polymers9436
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-109 kcal/mol
Surface area31060 Å2
MethodPISA
2
D: Purine nucleoside phosphorylase
E: Purine nucleoside phosphorylase
F: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,80411
Polymers100,6693
Non-polymers1,1358
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9300 Å2
ΔGint-136 kcal/mol
Surface area31740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.883, 111.120, 97.963
Angle α, β, γ (deg.)90.00, 108.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Purine nucleoside phosphorylase


Mass: 33556.227 Da / Num. of mol.: 6 / Mutation: S42E, H98R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis NRRL Y-1140 (yeast)
Gene: KLLA0_C16621g / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pRIL / References: UniProt: Q6CSZ6
#2: Chemical
ChemComp-IM5 / 2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one / DADMe-ImmG


Mass: 279.295 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H17N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% (w/v) PEG 3,350, 0.2 M Lithium sulphate and 0.1 M BIS-TRIS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 31, 2013 / Details: M
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 124549 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.128 / Χ2: 1.179 / Net I/σ(I): 10.1 / Num. measured all: 467792
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.99-2.023.70.98461791.303199.9
2.02-2.063.70.80161731.322199.9
2.06-2.13.70.72562531.3691100
2.1-2.143.70.61962001.3211100
2.14-2.193.70.51561881.2781100
2.19-2.243.70.45462281.2771100
2.24-2.33.80.38761891.3011100
2.3-2.363.80.35662361.2641100
2.36-2.433.80.29662331.1991100
2.43-2.513.80.25262131.1861100
2.51-2.63.80.22462101.1851100
2.6-2.73.80.18361861.1291100
2.7-2.823.80.15662431.1431100
2.82-2.973.80.13662251.0961100
2.97-3.163.80.11762421.0831100
3.16-3.43.80.10862221.0581100
3.4-3.743.80.10162581.0481100
3.74-4.293.70.092626811100
4.29-5.43.70.08762550.9671100
5.4-503.80.08963481.057199.4

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data scaling
CBASSdata collection
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→47.68 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2271 6248 5.02 %
Rwork0.1943 --
obs0.196 124374 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→47.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12974 0 130 313 13417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018
X-RAY DIFFRACTIONf_angle_d1.501
X-RAY DIFFRACTIONf_dihedral_angle_d7.2911895
X-RAY DIFFRACTIONf_chiral_restr0.082073
X-RAY DIFFRACTIONf_plane_restr0.0132336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.010.38562090.33283797X-RAY DIFFRACTION97
2.01-2.040.36822370.30573902X-RAY DIFFRACTION100
2.04-2.060.27721860.27723901X-RAY DIFFRACTION100
2.06-2.090.3332260.28463922X-RAY DIFFRACTION100
2.09-2.110.31922270.27673891X-RAY DIFFRACTION100
2.11-2.140.32522230.25533935X-RAY DIFFRACTION100
2.14-2.170.2792090.2533916X-RAY DIFFRACTION100
2.17-2.210.28981910.24173911X-RAY DIFFRACTION100
2.21-2.240.3192080.23773978X-RAY DIFFRACTION100
2.24-2.280.25182030.22963942X-RAY DIFFRACTION100
2.28-2.320.2612070.22123905X-RAY DIFFRACTION100
2.32-2.360.27192140.22143938X-RAY DIFFRACTION100
2.36-2.40.27661720.22523937X-RAY DIFFRACTION100
2.41-2.450.24212020.21683951X-RAY DIFFRACTION100
2.45-2.510.22662000.20483958X-RAY DIFFRACTION100
2.51-2.570.2432000.21343919X-RAY DIFFRACTION100
2.57-2.630.23872350.20913892X-RAY DIFFRACTION100
2.63-2.70.25512220.20153952X-RAY DIFFRACTION100
2.7-2.780.26372110.20353965X-RAY DIFFRACTION100
2.78-2.870.23791970.20023917X-RAY DIFFRACTION100
2.87-2.970.25832270.20333943X-RAY DIFFRACTION100
2.97-3.090.24052040.20693944X-RAY DIFFRACTION100
3.09-3.230.22582020.2023966X-RAY DIFFRACTION100
3.23-3.40.22941960.18833953X-RAY DIFFRACTION100
3.4-3.620.21312270.18793948X-RAY DIFFRACTION100
3.62-3.90.21311910.16923994X-RAY DIFFRACTION100
3.9-4.290.17752050.14853978X-RAY DIFFRACTION100
4.29-4.910.1682100.14293954X-RAY DIFFRACTION100
4.91-6.180.18982110.17593988X-RAY DIFFRACTION100
6.18-47.680.17261960.16754029X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.3307-0.023-0.81612.51320.67542.30410.17540.6272-0.6959-0.4615-0.29180.11560.2430.05190.02550.43960.1424-0.08730.4926-0.12720.407120.4687-14.412634.1701
26.20110.5004-0.41422.90650.94123.36840.46831.2974-0.0478-0.8167-0.2462-0.0885-0.2780.33720.00520.54010.15940.03870.5685-0.01170.3269122.2817-8.505831.8911
31.58660.22570.2881.5279-0.10.99340.07810.3236-0.229-0.216-0.03460.08950.16510.3998-0.03970.2970.0399-0.01120.3565-0.01850.3198115.1243-3.576437.4645
41.3773-0.16420.27220.708-0.08761.44390.01720.09110.0811-0.0035-0.0406-0.1303-0.14640.53140.01950.1782-0.04820.00810.37530.00920.2356120.33759.068343.2104
53.915-0.0621-0.26282.76630.71233.88070.1099-0.1021-0.6415-0.1298-0.09660.28710.4176-0.4629-0.00070.2897-0.0276-0.07040.36510.03540.501272.8693-0.247550.5911
63.8326-1.388-0.10751.09150.00170.29530.22950.3814-0.2676-0.1823-0.1830.2034-0.2074-0.2876-0.00650.20750.0327-0.01410.29560.03610.365183.60845.652947.2564
73.9219-0.4367-0.75741.3312-0.18642.37950.06420.08840.3891-0.02020.00870.0364-0.3377-0.4090.01170.2517-0.00640.02350.1705-0.01710.331689.67116.5457.5183
82.496-0.04640.09390.605-0.08431.78690.0901-0.19830.04510.058-0.01550.0023-0.05080.0691-0.07020.2004-0.02870.020.1608-0.00250.22496.64438.652859.2199
94.3318-1.52910.31034.07310.80043.76230.07820.5246-0.1097-0.4937-0.08190.2787-0.22620.231-0.03180.39620.0751-0.07380.5568-0.00910.3407101.64917.02496.858
102.78520.0311-0.11661.73751.20582.88660.23470.60210.1732-0.7157-0.05960.2289-1.0521-0.1285-0.04660.75930.0907-0.04190.48130.13950.498796.628831.534411.2749
112.087-1.6959-0.12873.28050.40492.81880.12270.2328-0.0082-0.3899-0.2426-0.0008-0.4733-0.01090.00160.4853-0.0006-0.02630.48310.14770.3097103.61325.482614.9376
121.2003-0.3562-0.16190.32220.65131.91670.06240.12790.3506-0.34910.0025-0.0518-0.74940.33320.01640.5157-0.12860.00020.34520.10590.3737106.922729.995730.5016
132.6941-2.0713-3.20683.61022.15783.9151-0.0088-0.22180.2087-0.2759-0.1580.4309-0.4202-0.56880.20990.3456-0.0179-0.02340.19290.07070.418796.930623.999945.2396
141.1136-0.6161-0.12331.18281.0443.6579-0.02040.07660.2906-0.35090.04130.1368-0.71620.5773-0.00770.3803-0.1057-0.03230.35810.13470.3946105.937424.641428.6331
150.75710.3829-1.33870.8243-0.91254.0499-0.1745-0.02090.05170.0899-0.21620.1825-0.87290.03040.1960.5715-0.0048-0.01060.30760.07840.588995.727231.951943.7136
161.56451.4665-0.55113.6981-0.99315.4633-0.48030.25850.5543-0.3153-0.39250.1009-0.6295-0.01380.30991.4364-0.1251-0.19720.4160.1820.5216100.003542.869822.0765
171.38990.3522-0.96742.0341-0.67952.6193-0.1350.1558-0.5871-0.0885-0.0356-0.53620.62320.50080.14790.54160.1839-0.02260.5206-0.04450.530592.79532.0909-1.6846
182.53650.34980.38280.5297-0.20610.90790.0599-0.0834-0.4021-0.0228-0.0637-0.20930.1760.159-0.05440.38440.0663-0.03150.3972-0.02640.352282.59746.90131.016
194.6511.2571-1.47432.6056-0.31232.66790.01450.15030.3148-0.10030.0068-0.0441-0.15090.39280.05630.30470.0640.00590.2976-0.00860.263875.234417.5585-8.5887
202.02070.3280.31090.9923-0.06781.59870.03920.3449-0.1362-0.13170.0153-0.05130.24540.1394-0.04910.34690.0554-0.00330.3044-0.04250.222369.32468.9391-10.811
216.11891.0238-1.68522.0852-1.913.3610.0524-0.7931-1.6099-0.05-0.3397-0.83020.5450.58410.22850.95020.0623-0.01450.61340.27110.854159.8287-20.420812.5323
223.42990.5681-0.90081.8539-0.78161.46740.1129-0.6243-1.22180.07020.00520.21041.1469-0.7927-0.03831.0733-0.3662-0.03480.63040.19020.838340.5022-18.049710.5933
235.5879-0.5375-0.67041.6117-1.91772.58530.0053-1.3783-0.69030.5041-0.1389-0.14750.2178-0.22760.02220.959-0.2660.07980.61770.22460.507348.4669-16.361517.0931
241.2724-0.3069-0.04611.24730.30521.0465-0.0306-0.2125-0.45470.11090.06280.03010.7846-0.3027-0.00040.6601-0.0861-0.00860.30940.04450.42250.1182-8.68629.5935
251.5232-0.0527-0.18161.05140.21381.7856-0.04970.1097-0.1389-0.14710.00510.1080.3724-0.35520.03520.3529-0.0674-0.02280.289-0.00550.231549.19763.24252.1108
261.67920.72640.07061.12840.21682.0773-0.1075-0.06020.3039-0.1112-0.04150.3935-0.2576-0.53280.12160.24280.0417-0.07030.4706-0.02790.29341.991719.312511.9517
272.02190.59450.98622.29141.00352.42630.0557-0.2604-0.3864-0.0527-0.1310.10210.6818-0.85170.10440.5024-0.2469-0.01370.70080.04340.450534.6565-2.48579.1776
282.44050.51071.22834.5387-0.85971.93760.0186-0.4812-0.14310.42530.0681-0.4189-0.0168-0.18-0.03420.27480.0418-0.0550.4375-0.02610.319962.748619.373640.2889
292.92930.27161.23563.9917-0.911.8176-0.0584-0.0760.08980.4148-0.0731-0.623-0.19430.14830.03980.26030.0201-0.04970.3667-0.01690.297865.798125.149936.4441
300.49850.10130.32871.54980.32281.27280.0015-0.16240.0961-0.12950.03740.0425-0.1674-0.2421-0.0420.20240.03820.00890.2644-0.0310.254756.128926.708219.9157
312.05970.9788-2.28284.3579-1.63972.6086-0.0077-0.10640.125-0.24550.015-0.59380.16630.52330.06620.35270.05910.01520.2673-0.07450.331666.926323.29834.1897
320.3943-0.70220.17680.24690.30451.9849-0.009-0.03770.237-0.1350.0782-0.0793-0.31310.0002-0.0750.29480.00450.0060.2532-0.03590.321762.576630.517817.2597
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 64 )
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 94 )
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 132 )
4X-RAY DIFFRACTION4chain 'A' and (resid 133 through 306 )
5X-RAY DIFFRACTION5chain 'B' and (resid 8 through 94 )
6X-RAY DIFFRACTION6chain 'B' and (resid 95 through 132 )
7X-RAY DIFFRACTION7chain 'B' and (resid 133 through 193 )
8X-RAY DIFFRACTION8chain 'B' and (resid 194 through 306 )
9X-RAY DIFFRACTION9chain 'C' and (resid 5 through 27 )
10X-RAY DIFFRACTION10chain 'C' and (resid 28 through 85 )
11X-RAY DIFFRACTION11chain 'C' and (resid 86 through 122 )
12X-RAY DIFFRACTION12chain 'C' and (resid 123 through 207 )
13X-RAY DIFFRACTION13chain 'C' and (resid 208 through 224 )
14X-RAY DIFFRACTION14chain 'C' and (resid 225 through 246 )
15X-RAY DIFFRACTION15chain 'C' and (resid 247 through 288 )
16X-RAY DIFFRACTION16chain 'C' and (resid 289 through 306 )
17X-RAY DIFFRACTION17chain 'D' and (resid 4 through 94 )
18X-RAY DIFFRACTION18chain 'D' and (resid 95 through 132 )
19X-RAY DIFFRACTION19chain 'D' and (resid 133 through 193 )
20X-RAY DIFFRACTION20chain 'D' and (resid 194 through 306 )
21X-RAY DIFFRACTION21chain 'E' and (resid 5 through 25 )
22X-RAY DIFFRACTION22chain 'E' and (resid 26 through 57 )
23X-RAY DIFFRACTION23chain 'E' and (resid 58 through 84 )
24X-RAY DIFFRACTION24chain 'E' and (resid 85 through 132 )
25X-RAY DIFFRACTION25chain 'E' and (resid 133 through 246 )
26X-RAY DIFFRACTION26chain 'E' and (resid 247 through 280 )
27X-RAY DIFFRACTION27chain 'E' and (resid 281 through 306 )
28X-RAY DIFFRACTION28chain 'F' and (resid 5 through 44 )
29X-RAY DIFFRACTION29chain 'F' and (resid 45 through 118 )
30X-RAY DIFFRACTION30chain 'F' and (resid 119 through 207 )
31X-RAY DIFFRACTION31chain 'F' and (resid 208 through 224 )
32X-RAY DIFFRACTION32chain 'F' and (resid 225 through 306 )

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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