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- PDB-4tym: Crystal structure of purine nucleoside phosphorylase from Strepto... -

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Basic information

Entry
Database: PDB / ID: 4tym
TitleCrystal structure of purine nucleoside phosphorylase from Streptococcus agalactiae 2603V/R, NYSGRC Target 030935
ComponentsPurine nucleoside phosphorylase DeoD-type
KeywordsTRANSFERASE / PROTEIN STRUCTURE INITIATIVE / PSI-Biology / NEW YORK STRUCTURAL GENOMICS RESEARCH CONSORTIUM / NYSGRC
Function / homologyNucleoside phosphorylase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesStreptococcus agalactiae LMG 15084 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.399 Å
AuthorsMalashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. ...Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Love, J. / Fiser, A. / Seidel, R. / Bonanno, J.B. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To Be Published
Title: Crystal structure of purine nucleoside phosphorylase from Streptococcus agalactiae 2603V/R, NYSGRC Target 030935.
Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. ...Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Love, J. / Fiser, A. / Seidel, R. / Bonanno, J.B. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
History
DepositionJul 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase DeoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5744
Polymers29,2861
Non-polymers2883
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Purine nucleoside phosphorylase DeoD-type
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)177,44624
Polymers175,7176
Non-polymers1,72918
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area23800 Å2
ΔGint-332 kcal/mol
Surface area48990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.552, 156.552, 52.090
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-411-

HOH

21A-417-

HOH

31A-427-

HOH

Detailsbiological unit is the same as asym.

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Components

#1: Protein Purine nucleoside phosphorylase DeoD-type / PNP


Mass: 29286.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae LMG 15084 (bacteria)
Gene: deoD, SAG0083_03075 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL
References: UniProt: S9I310, purine-nucleoside phosphorylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
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: 3.16 Å3/Da / Density % sol: 61.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M lithium sulfate, 0.1 M Tris:HCl, pH 7.0. 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9791 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 3.9 % / Number: 126748 / Rmerge(I) obs: 0.133 / Χ2: 1.05 / D res high: 2.2 Å / D res low: 50 Å / Num. obs: 32265 / % possible obs: 88.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
5.975010.0650.7544.5
4.745.9710.0881.0864.5
4.144.7410.0830.9624.7
3.764.1410.0961.0154.8
3.493.7610.1161.0474.8
3.293.4910.141.0814.8
3.123.2910.1751.1114.8
2.993.1210.221.1024.6
2.872.9910.2831.1074.5
2.772.8710.3971.0644.4
2.692.7710.5141.0844.3
2.612.6910.551.0874.1
2.542.6110.6211.0663.8
2.482.5410.7191.0873.1
2.422.4810.621.0422.5
2.372.4210.7031.1032.3
2.322.3710.7531.0892.2
2.282.3210.7631.0611.9
2.242.2810.6551.1261.9
2.22.2410.9481.0871.8
ReflectionResolution: 2.2→50 Å / Num. obs: 32265 / % possible obs: 88.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 38.84 Å2 / Rmerge(I) obs: 0.133 / Χ2: 1.048 / Net I/av σ(I): 8.954 / Net I/σ(I): 7.3 / Num. measured all: 126748
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.2-2.241.80.9488031.08743.9
2.24-2.281.90.6559361.12652
2.28-2.321.90.76310941.06159.9
2.32-2.372.20.75311631.08963.8
2.37-2.422.30.70314101.10378.7
2.42-2.482.50.6215831.04286.8
2.48-2.543.10.71917721.08797.8
2.54-2.613.80.62118311.06699.6
2.61-2.694.10.5517901.08799.7
2.69-2.774.30.51417881.08499.4
2.77-2.874.40.39718031.06499.4
2.87-2.994.50.28318191.10799.7
2.99-3.124.60.2218061.10299.8
3.12-3.294.80.17518221.11199.9
3.29-3.494.80.1418221.08199.9
3.49-3.764.80.11618201.04799.9
3.76-4.144.80.09617941.01599.9
4.14-4.744.70.08318400.96299.9
4.74-5.974.50.08817881.08699.6
5.97-504.50.06517810.75496.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
SHELXphasing
RESOLVEphasing
PDB_EXTRACT3.14data extraction
Cootmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.399→33.895 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 23.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1926 1311 4.72 %
Rwork0.1664 26475 -
obs0.1677 27786 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 164.89 Å2 / Biso mean: 51.8877 Å2 / Biso min: 18.34 Å2
Refinement stepCycle: final / Resolution: 2.399→33.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1820 0 15 91 1926
Biso mean--106.34 51.14 -
Num. residues----235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081865
X-RAY DIFFRACTIONf_angle_d1.0882529
X-RAY DIFFRACTIONf_chiral_restr0.044288
X-RAY DIFFRACTIONf_plane_restr0.004327
X-RAY DIFFRACTIONf_dihedral_angle_d15.643678
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.399-2.49530.32331460.28292790293694
2.4953-2.60880.26921430.247129753118100
2.6088-2.74630.2971290.223229783107100
2.7463-2.91830.23171610.213429173078100
2.9183-3.14340.20391460.17829493095100
3.1434-3.45950.18041270.153129983125100
3.4595-3.95940.16661540.138529453099100
3.9594-4.98590.15131470.117829593106100
4.9859-33.89790.17481580.168129643122100
Refinement TLS params.Method: refined / Origin x: 48.8158 Å / Origin y: 45.9188 Å / Origin z: 11.8464 Å
111213212223313233
T0.245 Å20.0082 Å2-0.0151 Å2-0.318 Å2-0.073 Å2--0.3335 Å2
L2.8139 °2-0.733 °2-0.6959 °2-2.499 °20.5119 °2--1.2341 °2
S-0.0095 Å °0.2871 Å °0.0123 Å °-0.1763 Å °-0.1397 Å °0.4254 Å °-0.029 Å °-0.3429 Å °0.1357 Å °
Refinement TLS groupSelection details: (chain A and resseq 24:258)

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