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- PDB-5cxs: Crystal Structure of Isoform 2 of Purine Nucleoside Phosphorylase... -

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Basic information

Entry
Database: PDB / ID: 5cxs
TitleCrystal Structure of Isoform 2 of Purine Nucleoside Phosphorylase complexed with MES
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE
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 / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsTorini, J.R. / Romanello, L. / Bird, L. / Owens, R. / Brandao-Neto, J. / Pereira, H.M.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2012/14223-9 Brazil
CitationJournal: PLoS ONE / Year: 2018
Title: The molecular structure of Schistosoma mansoni PNP isoform 2 provides insights into the nucleoside selectivity of PNPs.
Authors: Torini, J.R. / Romanello, L. / Batista, F.A.H. / Serrao, V.H.B. / Faheem, M. / Zeraik, A.E. / Bird, L. / Nettleship, J. / Reddivari, Y. / Owens, R. / DeMarco, R. / Borges, J.C. / Brandao-Neto, J. / Pereira, H.D.
History
DepositionJul 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: 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: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5552
Polymers31,3591
Non-polymers1951
Water3,801211
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)94,6646
Polymers94,0783
Non-polymers5863
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area8980 Å2
ΔGint-33 kcal/mol
Surface area30380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.847, 97.847, 97.847
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-554-

HOH

21A-607-

HOH

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Components

#1: Protein Purine nucleoside phosphorylase / Inosine-guanosine phosphorylase


Mass: 31359.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: Smp_179110 / Plasmid: pOPINS3C / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo
References: UniProt: G4VP83, purine-nucleoside phosphorylase
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.49 Å3/Da / Density % sol: 50.59 % / Description: Cubic form
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% PEG 4000, 20% Glycerol, 30mM diethyleneglycol 30mM tetraethyleneglycol, 30mM pentaethyleneglycol, 100mM Mes/Imidazol pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.74→43.73 Å / Num. all: 32239 / Num. obs: 32239 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 17.33 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 25.5 / Scaling rejects: 2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-IDRejects% possible all
1.74-1.7910.50.72310100
7.78-43.7310.20.0231099

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
xia2data scaling
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FAZ

3faz


Resolution: 1.75→24.462 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1911 1598 5.04 %Random selection
Rwork0.15 30083 --
obs0.152 31681 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.4 Å2 / Biso mean: 23.6043 Å2 / Biso min: 6.36 Å2
Refinement stepCycle: final / Resolution: 1.75→24.462 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 12 211 2385
Biso mean--35.71 34.43 -
Num. residues----283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182222
X-RAY DIFFRACTIONf_angle_d1.6943013
X-RAY DIFFRACTIONf_chiral_restr0.104351
X-RAY DIFFRACTIONf_plane_restr0.009389
X-RAY DIFFRACTIONf_dihedral_angle_d14.363834
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7503-1.80680.2621450.211627012846
1.8068-1.87140.26081390.180226952834
1.8714-1.94630.22451530.169227002853
1.9463-2.03480.18881340.153727292863
2.0348-2.1420.18651370.150627082845
2.142-2.27610.1971590.14727262885
2.2761-2.45170.19381700.149826862856
2.4517-2.69820.21341410.154127252866
2.6982-3.0880.17321370.145427612898
3.088-3.8880.18461590.143127582917
3.888-24.46410.15911240.13728943018
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)
15.7484-3.94781.31327.7171-0.2734.23060.15370.2238-0.5142-0.1812-0.05960.4910.2596-0.4472-0.05930.1291-0.02890.05170.203-0.01130.1963-28.465-37.6543-3.4545
24.70621.9879-1.57854.6285-1.05442.21730.098-0.3192-0.89920.1536-0.0748-0.32860.45010.1888-0.00540.24260.0376-0.0460.21680.06860.2544-11.4887-40.46526.0847
32.71570.04110.861.83521.13451.7770.07190.0662-0.3733-0.07460.0571-0.15620.250.149-0.10810.19780.01720.04650.11370.00450.2563-15.8396-40.5627-2.5114
42.89971.5265-2.17240.9682-1.5012.70040.05540.0184-0.1470.0298-0.0563-0.0903-0.01290.03730.00190.14110.01150.02710.0940.00090.1627-17.6138-29.3367-5.4143
52.1156-0.35620.38061.0259-0.29211.132-0.0659-0.1712-0.00840.14810.0410.0175-0.05920.05250.01820.11560.01520.02320.0789-0.00010.0515-12.4059-19.72952.4139
62.8157-0.75321.8293.7479-1.05896.2489-0.1173-0.8029-0.07640.7140.0857-0.0524-0.1188-0.1786-0.0050.2793-0.024-0.00680.28930.02690.1106-5.9247-25.149819.1032
71.06550.1885-0.04271.0299-0.391.0866-0.0084-0.06920.01290.1543-0.0162-0.0817-0.04520.13110.01970.11980.0276-0.0060.1060.00560.0826-3.9606-18.89541.255
86.82592.6222-1.85382.9282-1.87522.111-0.09060.2111-0.1091-0.1397-0.1388-0.36440.11280.21860.21760.13460.0516-0.00150.19070.01950.09994.9041-20.4371-0.6158
95.92250.9122-4.01962.7002-0.76716.84610.0676-0.0092-0.3945-0.111-0.1102-0.00680.2108-0.0210.05980.25120.0789-0.07260.17990.05490.1507-1.7423-33.72128.9821
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 23 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 47 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 84 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 108 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 109 through 169 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 170 through 182 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 183 through 235 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 236 through 258 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 259 through 287 )A0

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