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- PDB-8swt: Structure of Bacteroides fragilis PNP bound to transition state a... -

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Basic information

Entry
Database: PDB / ID: 8swt
TitleStructure of Bacteroides fragilis PNP bound to transition state analog IMMUCILLIN H 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
Similarity search - Function
Purine nucleoside phosphorylase I, inosine/guanosine-specific / Purine nucleoside phosphorylase / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily
Similarity search - Domain/homology
Chem-IMH / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesBacteroides fragilis NCTC 9343 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9356
Polymers65,2112
Non-polymers7254
Water8,917495
1
A: Purine nucleoside phosphorylase
hetero molecules

A: Purine nucleoside phosphorylase
hetero molecules

A: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9039
Polymers97,8163
Non-polymers1,0876
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area9130 Å2
ΔGint-93 kcal/mol
Surface area29400 Å2
MethodPISA
2
B: Purine nucleoside phosphorylase
hetero molecules

B: Purine nucleoside phosphorylase
hetero molecules

B: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9039
Polymers97,8163
Non-polymers1,0876
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area8590 Å2
ΔGint-92 kcal/mol
Surface area28320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.424, 79.424, 166.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-650-

HOH

21B-613-

HOH

31B-642-

HOH

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Components

#1: Protein Purine nucleoside phosphorylase


Mass: 32605.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria)
Gene: punA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pRIL / References: UniProt: Q5LAA3
#2: Chemical ChemComp-IMH / 1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL / Forodesine / Immucillin H


Mass: 266.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H14N4O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 495 / 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: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% (w/v) PEG 8,000, 0.2 M Magnesium acetate and 0.1 M Sodium cacodylate

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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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.66→19.9 Å / Num. obs: 67700 / % possible obs: 96.8 % / Redundancy: 9.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.043 / Rrim(I) all: 0.133 / Χ2: 0.96 / Net I/σ(I): 14.1 / Num. measured all: 642801
Reflection shellResolution: 1.66→1.69 Å / % possible obs: 100 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.456 / Num. measured all: 30423 / Num. unique obs: 3444 / CC1/2: 0.951 / Rpim(I) all: 0.162 / Rrim(I) all: 0.484 / Χ2: 0.79 / Net I/σ(I) obs: 5.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→19.9 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1732 3338 4.93 %
Rwork0.1471 --
obs0.1485 67654 96.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.66→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4272 0 48 495 4815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02
X-RAY DIFFRACTIONf_angle_d1.733
X-RAY DIFFRACTIONf_dihedral_angle_d5.771595
X-RAY DIFFRACTIONf_chiral_restr0.108668
X-RAY DIFFRACTIONf_plane_restr0.014766
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.680.21211460.15132727X-RAY DIFFRACTION100
1.68-1.710.19431180.14562796X-RAY DIFFRACTION100
1.71-1.740.18371500.14042758X-RAY DIFFRACTION100
1.74-1.760.15871460.13752790X-RAY DIFFRACTION100
1.76-1.790.19041380.13642721X-RAY DIFFRACTION100
1.79-1.830.16511590.1372765X-RAY DIFFRACTION100
1.83-1.860.19771690.14192744X-RAY DIFFRACTION100
1.86-1.90.19071260.14782777X-RAY DIFFRACTION100
1.9-1.940.2181850.14451835X-RAY DIFFRACTION66
1.94-1.990.18211480.15362768X-RAY DIFFRACTION100
1.99-2.040.23451430.14862765X-RAY DIFFRACTION100
2.04-2.090.17441210.14052784X-RAY DIFFRACTION100
2.09-2.150.15591430.13722767X-RAY DIFFRACTION100
2.15-2.220.17591290.1462771X-RAY DIFFRACTION100
2.22-2.30.19541120.1471727X-RAY DIFFRACTION64
2.3-2.390.16921380.1512785X-RAY DIFFRACTION100
2.39-2.50.22321210.15932786X-RAY DIFFRACTION100
2.5-2.630.19311420.16482773X-RAY DIFFRACTION100
2.63-2.80.1811480.16542753X-RAY DIFFRACTION100
2.8-3.010.18741390.15572764X-RAY DIFFRACTION100
3.01-3.320.16241530.15142782X-RAY DIFFRACTION100
3.32-3.790.13651530.1432763X-RAY DIFFRACTION100
3.79-4.760.14031770.12732591X-RAY DIFFRACTION95
4.77-19.90.17731340.15062824X-RAY DIFFRACTION100
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)
10.810.1436-0.27280.8345-0.33891.23130.01570.08630.0205-0.0376-0.01710.0358-0.1361-0.1164-0.01180.11760.0111-0.01790.0980.00250.1075-11.4133-19.7365-11.5518
20.450.3197-0.84681.7231-1.1422.87440.01210.04280.1005-0.00330.13280.1440.1165-0.1998-0.13650.09880.0044-0.01450.12730.00860.1301-16.0333-29.9276-11.7587
30.50990.0214-0.07930.5833-0.17770.74940.0064-0.03780.05030.02960.00540.0154-0.0976-0.0493-0.00860.07010.009-0.00620.0524-0.01010.0663-9.2982-28.46243.9202
41.7042-0.2209-0.45130.51130.26881.913-0.003-0.13510.11450.0137-0.02490.0246-0.1123-0.06250.02460.10260.0128-0.00970.1038-0.02610.1226-9.251-18.869556.0096
50.798-0.6725-0.80460.86770.27762.26880.0544-0.00920.0953-0.07770.043-0.042500.1583-0.08980.1156-0.01460.00010.128-0.02240.13351.1082-23.507356.0492
60.67690.0122-0.08090.7653-0.02460.9759-0.01520.00530.0784-0.00620.00660.0389-0.1375-0.04950.00240.06510.0115-0.0110.0469-0.00220.0787-5.7627-24.832244.9468
71.31260.1561-0.26481.1473-0.10330.718-0.0011-0.03780.0452-0.0315-0.00270.0729-0.0072-0.05080.00780.0730.00660.00110.045-0.00750.0754-14.7846-37.726146.6081
80.4776-0.0932-0.06840.6251-0.04760.8005-0.00160.04840.07-0.04750.0090.0164-0.1555-0.0236-0.00380.08810.0051-0.0090.05260.00580.0676-2.0725-25.331735.6864
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 272 )
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 50 )
5X-RAY DIFFRACTION5chain 'B' and (resid 51 through 64 )
6X-RAY DIFFRACTION6chain 'B' and (resid 65 through 136 )
7X-RAY DIFFRACTION7chain 'B' and (resid 137 through 161 )
8X-RAY DIFFRACTION8chain 'B' and (resid 162 through 272 )

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