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- PDB-6xz2: Crystal structure of E. Coli purine nucleoside phosphorylase muta... -

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Basic information

Entry
Database: PDB / ID: 6xz2
TitleCrystal structure of E. Coli purine nucleoside phosphorylase mutant Y160W with SO4 and Formycin A
ComponentsPurine nucleoside phosphorylase DeoD-type
KeywordsTRANSFERASE / trimer of dimers / single tryptophan mutant / protein-inhibitor complex
Function / homology
Function and homology information


purine nucleoside interconversion / guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / purine nucleoside catabolic process / DNA damage response / identical protein binding / membrane / cytosol
Similarity search - Function
Purine nucleoside phosphorylase DeoD-type / Nucleoside phosphorylase, conserved site / Purine and other phosphorylases family 1 signature. / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily
Similarity search - Domain/homology
Chem-FMC / Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65000304482 Å
AuthorsNarczyk, M. / Bzowska, A.
CitationJournal: Sci Rep / Year: 2021
Title: Single tryptophan Y160W mutant of homooligomeric E. coli purine nucleoside phosphorylase implies that dimers forming the hexamer are functionally not equivalent.
Authors: Narczyk, M. / Mioduszewski, L. / Oksiejuk, A. / Winiewska-Szajewska, M. / Wielgus-Kutrowska, B. / Gojdz, A. / Ciesla, J. / Bzowska, A.
History
DepositionJan 31, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation / citation_author
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 / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: 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 DeoD-type
B: Purine nucleoside phosphorylase DeoD-type
C: Purine nucleoside phosphorylase DeoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7897
Polymers77,2343
Non-polymers5554
Water5,477304
1
A: Purine nucleoside phosphorylase DeoD-type
B: Purine nucleoside phosphorylase DeoD-type
C: Purine nucleoside phosphorylase DeoD-type
hetero molecules

A: Purine nucleoside phosphorylase DeoD-type
B: Purine nucleoside phosphorylase DeoD-type
C: Purine nucleoside phosphorylase DeoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,57914
Polymers154,4686
Non-polymers1,1118
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area23650 Å2
ΔGint-243 kcal/mol
Surface area46140 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8150 Å2
ΔGint-97 kcal/mol
Surface area26740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.475, 120.475, 239.799
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-426-

HOH

21A-429-

HOH

31A-501-

HOH

41B-479-

HOH

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Components

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


Mass: 25744.668 Da / Num. of mol.: 3 / Mutation: Y160W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: deoD, pup, b4384, JW4347 / Production host: Escherichia coli (E. coli)
References: UniProt: P0ABP8, purine-nucleoside phosphorylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FMC / (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.25 Å3/Da / Density % sol: 62.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 50 mM citrate buffer pH 5.2, 14 % ammonium sulphate (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.0064 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0064 Å / Relative weight: 1
ReflectionResolution: 1.65→104.3 Å / Num. obs: 123021 / % possible obs: 99.42 % / Redundancy: 99.8 % / Biso Wilson estimate: 22.4977063367 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.028 / Rrim(I) all: 0.177 / Net I/σ(I): 14.7
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 1.483 / Num. unique obs: 5869 / CC1/2: 0.821 / Rpim(I) all: 0.26 / Rrim(I) all: 1.507

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIX1.11.1_2575refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ecp

1ecp


Resolution: 1.65000304482→78.7072722459 Å / SU ML: 0.157720237261 / Cross valid method: FREE R-VALUE / σ(F): 1.35096088804 / Phase error: 18.312385071
RfactorNum. reflection% reflection
Rfree0.191874953474 6119 4.97779151685 %
Rwork0.179874338677 --
obs0.180478601074 122926 99.6562626672 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27.1661880984 Å2
Refinement stepCycle: LAST / Resolution: 1.65000304482→78.7072722459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5397 0 34 304 5735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005934448901235538
X-RAY DIFFRACTIONf_angle_d0.8155513382337474
X-RAY DIFFRACTIONf_chiral_restr0.058318116518850
X-RAY DIFFRACTIONf_plane_restr0.00502542371946961
X-RAY DIFFRACTIONf_dihedral_angle_d4.573833728234533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.66880.2469680107412090.2244173166313708X-RAY DIFFRACTION97.3893585281
1.6688-1.68840.2602963004831860.218081690043832X-RAY DIFFRACTION99.1609081935
1.6884-1.7090.2036211282242050.198115731373819X-RAY DIFFRACTION99.431677786
1.709-1.73060.2194086895361930.2034426861523807X-RAY DIFFRACTION99.4530084535
1.7306-1.75340.2201376700952270.1869057763963815X-RAY DIFFRACTION99.2632612967
1.7534-1.77740.2246126215822110.1889346486283827X-RAY DIFFRACTION99.4581280788
1.7774-1.80280.1814127382161980.1826348821463833X-RAY DIFFRACTION99.4817374136
1.8028-1.82970.2162657387971780.1817464139033875X-RAY DIFFRACTION99.5578481945
1.8297-1.85830.2059484706121860.1781348174113847X-RAY DIFFRACTION99.6540647393
1.8583-1.88880.1994542557041990.1829525850063855X-RAY DIFFRACTION99.5824121837
1.8888-1.92130.2304035322232050.1855333845143825X-RAY DIFFRACTION99.6784565916
1.9213-1.95630.2271535773372100.1738510035833849X-RAY DIFFRACTION99.7297297297
1.9563-1.99390.198719316441970.1839217374633858X-RAY DIFFRACTION99.7294638465
1.9939-2.03460.210060612272110.1764621601953854X-RAY DIFFRACTION99.315905204
2.0346-2.07890.2026176293262080.1813134127043865X-RAY DIFFRACTION99.8284313725
2.0789-2.12720.198835694871990.1768670614043867X-RAY DIFFRACTION99.8281365087
2.1272-2.18040.1870623376861900.1772426451433899X-RAY DIFFRACTION99.9755501222
2.1804-2.23940.2144600262531970.1790922607533886X-RAY DIFFRACTION99.9265785609
2.2394-2.30530.1978737178022150.177822640743866X-RAY DIFFRACTION99.9755022048
2.3053-2.37970.2155710907432140.1808835880743894X-RAY DIFFRACTION99.9756631784
2.3797-2.46480.1893293878281970.1782667040733919X-RAY DIFFRACTION100
2.4648-2.56340.1979689745812080.1871241266753908X-RAY DIFFRACTION100
2.5634-2.68010.1842582109182070.1801971241493923X-RAY DIFFRACTION100
2.6801-2.82140.1681354637211900.1944974032953924X-RAY DIFFRACTION99.9271314064
2.8214-2.99820.2037225731172020.1950593515963938X-RAY DIFFRACTION99.8071359691
2.9982-3.22970.2011869348362160.1873015520853944X-RAY DIFFRACTION100
3.2297-3.55470.1724159827031900.1806020493244006X-RAY DIFFRACTION100
3.5547-4.06910.1873453131131990.1620000850324028X-RAY DIFFRACTION100
4.0691-5.12650.1612004745992270.1535976082424057X-RAY DIFFRACTION99.9533364442
5.1265-78.70.190376057342450.193493519634279X-RAY DIFFRACTION99.6475770925

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