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- PDB-8swq: Structure of K. lactis PNP bound to transition state analog DADMe... -

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Basic information

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


nucleoside metabolic process / purine-nucleoside phosphorylase activity / purine-nucleoside phosphorylase / 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-DIH / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesKluyveromyces lactis NRRL Y-1140 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.979 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 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Nov 22, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)204,38420
Polymers202,3786
Non-polymers2,00614
Water12,520695
1
A: Purine nucleoside phosphorylase
B: Purine nucleoside phosphorylase
C: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,19210
Polymers101,1893
Non-polymers1,0037
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10480 Å2
ΔGint-99 kcal/mol
Surface area30600 Å2
MethodPISA
2
D: Purine nucleoside phosphorylase
E: Purine nucleoside phosphorylase
F: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,19210
Polymers101,1893
Non-polymers1,0037
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10420 Å2
ΔGint-99 kcal/mol
Surface area30070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.963, 110.788, 98.043
Angle α, β, γ (deg.)90.00, 108.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Purine nucleoside phosphorylase


Mass: 33729.617 Da / Num. of mol.: 6
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-DIH / 7-[[(3R,4R)-3-(hydroxymethyl)-4-oxidanyl-pyrrolidin-1-ium-1-yl]methyl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one


Mass: 265.288 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H17N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 695 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 46.51 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 25% (w/v) PEG 3,350, 0.2 M Ammonium sulphate and 0.11 M BIS-TRIS
PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 2, 2013
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.979→30 Å / Num. obs: 126431 / % possible obs: 99.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.119 / Χ2: 1.04 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.98-2.013.90.785124971.0641100
2.01-2.053.90.646124721.0681100
2.05-2.093.90.569124611.0831100
2.09-2.133.90.477125111.0551100
2.13-2.183.90.405123331.0491100
2.18-2.233.90.34124991.0471100
2.23-2.293.90.296124091.0911100
2.29-2.353.90.263124081.051100
2.35-2.423.90.23124651.0341100
2.42-2.493.90.197125211.0361100
2.49-2.583.90.176123921.0551100
2.58-2.693.90.15125241.0531100
2.69-2.813.90.128123981.0411100
2.81-2.963.90.117124631.0471100
2.96-3.143.90.109124151.0271100
3.14-3.383.90.108124571.0251100
3.38-3.723.90.103124530.9771100
3.72-4.263.90.081124830.9991100
4.26-5.363.90.067124161.0121100
5.36-303.80.06120620.997196.7

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.979→26.367 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.197 6316 5.01 %
Rwork0.1632 --
obs0.1649 125961 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.979→26.367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12734 0 130 695 13559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713191
X-RAY DIFFRACTIONf_angle_d1.25517892
X-RAY DIFFRACTIONf_dihedral_angle_d14.6124782
X-RAY DIFFRACTIONf_chiral_restr0.0832057
X-RAY DIFFRACTIONf_plane_restr0.0052289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9793-2.00180.24371870.20993736X-RAY DIFFRACTION93
2.0018-2.02540.25912120.20073993X-RAY DIFFRACTION100
2.0254-2.05010.26282100.20024000X-RAY DIFFRACTION100
2.0501-2.0760.23582010.19713976X-RAY DIFFRACTION100
2.076-2.10330.23512290.19223971X-RAY DIFFRACTION100
2.1033-2.13210.22332010.17934045X-RAY DIFFRACTION100
2.1321-2.16260.22371940.17183940X-RAY DIFFRACTION100
2.1626-2.19480.21642080.17664014X-RAY DIFFRACTION100
2.1948-2.22910.20572030.16614007X-RAY DIFFRACTION100
2.2291-2.26560.23361870.16683981X-RAY DIFFRACTION100
2.2656-2.30470.17092170.16664004X-RAY DIFFRACTION100
2.3047-2.34660.19492270.16153957X-RAY DIFFRACTION100
2.3466-2.39170.21562090.16394027X-RAY DIFFRACTION100
2.3917-2.44040.19071970.16943971X-RAY DIFFRACTION100
2.4404-2.49350.23812120.16724001X-RAY DIFFRACTION100
2.4935-2.55140.21932180.17284011X-RAY DIFFRACTION100
2.5514-2.61520.20091920.16473969X-RAY DIFFRACTION100
2.6152-2.68580.19392110.16084033X-RAY DIFFRACTION100
2.6858-2.76480.20182090.16623946X-RAY DIFFRACTION100
2.7648-2.85390.2142270.17274017X-RAY DIFFRACTION100
2.8539-2.95580.22752290.17333989X-RAY DIFFRACTION100
2.9558-3.0740.21932090.17113999X-RAY DIFFRACTION100
3.074-3.21360.19252130.17464012X-RAY DIFFRACTION100
3.2136-3.38270.18652180.17154005X-RAY DIFFRACTION100
3.3827-3.59420.20442080.16343994X-RAY DIFFRACTION100
3.5942-3.87090.17532160.14754017X-RAY DIFFRACTION100
3.8709-4.2590.15111980.13194056X-RAY DIFFRACTION100
4.259-4.87190.16212400.12523983X-RAY DIFFRACTION100
4.8719-6.12530.1842230.16064049X-RAY DIFFRACTION100
6.1253-26.3670.19322110.17413942X-RAY DIFFRACTION96
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)
13.165-0.0085-0.09340.66890.60350.91370.22070.7851-0.5364-0.4243-0.2001-0.02730.00770.0947-0.15280.33530.0681-0.04720.2834-0.11370.369689.0818-13.019126.0195
21.9805-0.22870.21380.9858-0.11350.7533-0.01520.08260.0292-0.0552-0.0116-0.0286-0.01310.14040.02620.1102-0.01350.00720.133700.13687.97525.9389135.0252
35.20972.6078-6.391.5122-3.54288.4971-0.02110.7172-0.6686-0.36850.00080.29450.5402-1.16930.16040.2969-0.0429-0.09110.4009-0.07210.386238.7566-0.2953132.5425
42.62940.295-0.15322.84651.01723.90720.0723-0.3302-0.47340.1423-0.05210.22570.4716-0.39860.00930.1934-0.0443-0.04330.2620.06970.351941.7421-0.6431147.6222
52.6748-0.13840.62350.3023-0.0060.94730.1310.0038-0.1203-0.0807-0.02250.0577-0.0388-0.1407-0.10870.1321-00.00540.1270.02830.21154.26116.6057144.6963
63.6154-0.3265-1.60411.32570.3243.28960.1560.57670.4267-0.1798-0.07510.1045-0.3027-0.3805-0.06840.15690.0087-0.00340.14510.04940.220660.033116.1768139.6026
73.27710.1868-0.22842.6435-1.10264.950.2632-0.4780.34690.42820.23450.2993-0.4372-0.5546-0.08430.20780.05320.10690.2592-0.07480.280849.04218.4598159.4135
82.3678-0.1684-0.05020.51740.03521.11910.0156-0.0920.09480.04410.00710.0362-0.05790.0382-0.0180.1213-0.01790.02510.0891-0.0010.14265.238411.0955149.1155
92.64251.17962.21190.61390.93351.92560.1853-0.3159-0.47260.40170.0591-0.1847-0.04960.3602-0.16660.21550.0397-0.01190.33690.03060.226985.37491.2604156.3067
106.4632-3.196-1.17873.80540.66113.2165-0.0585-0.3308-0.17710.23120.05770.1938-0.0197-0.1768-0.01840.1567-0.0670.01640.15660.03430.15153.94963.6609158.098
110.8033-0.07650.46382.2642-0.3561.19910.17630.50560.0992-0.5952-0.21270.4034-0.5253-0.05940.09450.47740.1275-0.07770.46320.05480.318567.382125.1607102.2544
122.2079-2.66791.4696.5723-1.60441.03330.13120.1583-0.00510.3472-0.08680.4513-0.7342-0.4326-0.13740.51520.0898-0.02770.44360.11440.255869.478426.3239107.5092
131.164-0.5743-0.0721.41690.30821.3860.04740.17390.3093-0.2124-0.10560.0364-0.37930.03150.02250.2441-0.0308-0.03470.16250.07350.285774.009828.6937124.2379
140.6030.2308-0.30182.0692-1.69093.0872-0.03020.05330.1517-0.1799-0.38740.0628-0.66590.16370.23590.57530.0766-0.10560.22230.02190.493665.076536.9633128.6678
153.99881.9195-0.50371.89050.32741.306-0.0472-0.4096-1.10060.37710.04020.03670.9079-0.0441-0.19021.0880.1527-0.27020.15480.45140.6147118.1594-20.6255105.7013
163.0446-0.01250.60462.1093-0.07431.44370.0603-0.8365-0.86960.1894-0.19560.18360.7595-0.45640.13180.8077-0.17420.08030.46810.11770.5418101.6099-17.6654105.0995
171.12630.0531-0.07340.97950.38881.5162-0.01630.0414-0.2165-0.0186-0.01310.04170.396-0.14950.02970.3224-0.0427-0.02740.18920.00060.1778107.50351.367697.4541
181.67670.44450.22952.56310.79712.1628-0.0481-0.09860.04130.0768-0.15110.42740.3433-0.54770.12030.2083-0.0592-0.01810.36480.01360.230494.83486.2527104.7768
194.25970.4823-4.56841.33370.09637.89370.28990.0782-0.6407-0.0288-0.2552-0.67510.45761.14140.07850.36220.1708-0.21150.42030.01730.4023154.50972.2901101.5373
203.04890.2856-1.11512.9976-0.40761.9343-0.1530.2596-0.4028-0.33230.0304-0.55750.56990.72040.07770.41340.17370.02690.6328-0.13570.4144153.71223.758583.9747
211.79630.5807-1.0592.4237-1.76644.1665-0.12030.2961-0.4934-0.1965-0.0559-0.38340.60280.3260.10490.38930.16630.02680.4662-0.0820.4307150.99360.606889.0663
222.60210.60850.3370.87520.22580.99850.04490.1328-0.2490.05670.012-0.16630.09130.2296-0.07130.3030.0722-0.00150.3106-0.05050.1793138.56767.892989.1945
233.96591.5933-2.6061.7669-0.83132.72720.2212-0.69630.13380.4547-0.2124-0.0188-0.27590.76730.02460.3121-0.0029-0.01780.3296-0.07830.1797131.575916.233494.8142
242.01380.2928-0.19560.66380.01881.19720.03160.34890.0263-0.07510.0466-0.01010.12070.1634-0.05940.26250.04860.00360.2716-0.02840.1187129.451212.681683.4629
254.24630.2734-0.76530.80050.0811.44430.12140.2034-0.0984-0.0922-0.0288-0.01720.27070.2446-0.07870.41390.0763-0.02920.3265-0.08950.1918129.0613.360676.3146
260.24910.0647-0.5048.28662.84572.51090.0444-0.2902-0.10750.77640.023-0.09370.08490.26450.16970.19950.0266-0.11060.31020.03960.2534121.552312.8763134.9693
272.55230.73741.04663.9504-1.12192.7004-0.048-0.16560.12810.36050.0052-0.504-0.21350.15040.04180.19280.0188-0.04930.2617-0.04280.1993124.475727.8243131.1373
281.99050.8310.975.73030.20542.27740.01140.050.0801-0.06960.0302-0.4229-0.16160.1278-0.09190.16940.0243-0.02020.2463-0.00920.1764121.135223.5274127.5643
290.66040.3335-0.03581.77650.16871.329-0.0082-0.08410.0752-0.18580.02910.0334-0.0961-0.1071-0.02470.13530.02740.00480.1718-0.01410.1406113.664424.4786113.414
300.74430.2746-0.17281.19320.33651.9639-0.06540.0690.0508-0.27540.1107-0.1162-0.11950.0218-0.02450.15930.01630.01330.1506-0.02380.1474118.888826.3043107.1908
310.9176-0.8438-0.46870.80671.13362.86340.31060.09020.1937-0.3656-0.0658-0.1563-0.81460.3905-0.0920.2947-0.02840.07160.2063-0.0140.2421125.570530.617199.1403
323.83442.6863-5.18935.5924-1.43859.1864-0.0043-0.2380.642-0.02850.0083-0.3515-0.6130.3571-0.20030.32580.0417-0.05440.2119-0.01840.3062120.400239.7664120.8696
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 89 )
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 306 )
3X-RAY DIFFRACTION3chain 'B' and (resid 5 through 27 )
4X-RAY DIFFRACTION4chain 'B' and (resid 28 through 89 )
5X-RAY DIFFRACTION5chain 'B' and (resid 90 through 144 )
6X-RAY DIFFRACTION6chain 'B' and (resid 145 through 180 )
7X-RAY DIFFRACTION7chain 'B' and (resid 181 through 193 )
8X-RAY DIFFRACTION8chain 'B' and (resid 194 through 267 )
9X-RAY DIFFRACTION9chain 'B' and (resid 268 through 280 )
10X-RAY DIFFRACTION10chain 'B' and (resid 281 through 306 )
11X-RAY DIFFRACTION11chain 'C' and (resid 5 through 78 )
12X-RAY DIFFRACTION12chain 'C' and (resid 79 through 118 )
13X-RAY DIFFRACTION13chain 'C' and (resid 119 through 257 )
14X-RAY DIFFRACTION14chain 'C' and (resid 258 through 306 )
15X-RAY DIFFRACTION15chain 'D' and (resid 5 through 25 )
16X-RAY DIFFRACTION16chain 'D' and (resid 26 through 89 )
17X-RAY DIFFRACTION17chain 'D' and (resid 90 through 267 )
18X-RAY DIFFRACTION18chain 'D' and (resid 268 through 306 )
19X-RAY DIFFRACTION19chain 'E' and (resid 8 through 24 )
20X-RAY DIFFRACTION20chain 'E' and (resid 25 through 57 )
21X-RAY DIFFRACTION21chain 'E' and (resid 58 through 89 )
22X-RAY DIFFRACTION22chain 'E' and (resid 90 through 144 )
23X-RAY DIFFRACTION23chain 'E' and (resid 145 through 180 )
24X-RAY DIFFRACTION24chain 'E' and (resid 181 through 267 )
25X-RAY DIFFRACTION25chain 'E' and (resid 268 through 306 )
26X-RAY DIFFRACTION26chain 'F' and (resid 5 through 27 )
27X-RAY DIFFRACTION27chain 'F' and (resid 28 through 78 )
28X-RAY DIFFRACTION28chain 'F' and (resid 79 through 118 )
29X-RAY DIFFRACTION29chain 'F' and (resid 119 through 193 )
30X-RAY DIFFRACTION30chain 'F' and (resid 194 through 246 )
31X-RAY DIFFRACTION31chain 'F' and (resid 247 through 286 )
32X-RAY DIFFRACTION32chain 'F' and (resid 287 through 306 )

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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