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- PDB-4d8x: Crystal structure of the hexameric purine nucleoside phosphorylas... -

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Basic information

Entry
Database: PDB / ID: 4d8x
TitleCrystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis in space group P6322 at pH 4.6
ComponentsPurine nucleoside phosphorylase deoD-type
KeywordsTRANSFERASE / Phosphorylase/hydrolase-like
Function / homology
Function and homology information


purine nucleoside catabolic process / purine-nucleoside phosphorylase activity / purine-nucleoside phosphorylase / cytosol
Similarity search - Function
Purine nucleoside phosphorylase DeoD-type / Nucleoside phosphorylase, conserved site / Purine and other phosphorylases family 1 signature. / 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 DeoD-type
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsSantos, C.R. / Meza, A.N. / Martins, N.H. / Giuseppe, P.O. / Murakami, M.T.
CitationJournal: Plos One / Year: 2012
Title: Insights into phosphate cooperativity and influence of substrate modifications on binding and catalysis of hexameric purine nucleoside phosphorylases.
Authors: de Giuseppe, P.O. / Martins, N.H. / Meza, A.N. / Dos Santos, C.R. / Pereira, H.D. / Murakami, M.T.
History
DepositionJan 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase deoD-type


Theoretical massNumber of molelcules
Total (without water)27,5621
Polymers27,5621
Non-polymers00
Water77543
1
A: Purine nucleoside phosphorylase deoD-type
x 6


Theoretical massNumber of molelcules
Total (without water)165,3736
Polymers165,3736
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/21
crystal symmetry operation11_454-x+y-1,y,-z-1/21
crystal symmetry operation12_554x,x-y,-z-1/21
Buried area20670 Å2
ΔGint-124 kcal/mol
Surface area46120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.805, 135.805, 57.019
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-307-

HOH

21A-326-

HOH

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Components

#1: Protein Purine nucleoside phosphorylase deoD-type / PNP / Purine nucleoside phosphorylase II / PU-NPase II


Mass: 27562.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU19630, deoD, punB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: O34925, purine-nucleoside phosphorylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THIS IS A CLONING ARTIFACT

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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: 2.75 Å3/Da / Density % sol: 55.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 4.6
Details: 0.1 M sodium acetate, 3.2 M sodium chloride, 5%(v/v) glycerol, pH 4.6, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.65→30 Å / Num. obs: 9359 / % possible obs: 99.1 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.1 / Χ2: 1.011 / Net I/σ(I): 11.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.65-2.746.20.489240.998199.9
2.74-2.856.40.3469210.972199.9
2.85-2.986.50.2559121.0521100
2.98-3.146.60.1759221.001199.8
3.14-3.346.50.1339251.027199.7
3.34-3.66.50.1039230.991199.1
3.6-3.966.60.0899311.009199.5
3.96-4.536.50.099401.01198.8
4.53-5.76.50.079521.007197.9
5.7-306.10.0510091.039196.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→29.17 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.886 / WRfactor Rfree: 0.2608 / WRfactor Rwork: 0.1897 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8123 / SU R Cruickshank DPI: 0.5634 / SU Rfree: 0.3217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.563 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2617 445 4.8 %RANDOM
Rwork0.1923 ---
obs0.1957 9286 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 81.94 Å2 / Biso mean: 40.0195 Å2 / Biso min: 11.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.04 Å20 Å2
2--0.07 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.65→29.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1761 0 0 43 1804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221808
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.9592451
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4695236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.11924.74478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.27115315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.586159
X-RAY DIFFRACTIONr_chiral_restr0.0930.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021347
X-RAY DIFFRACTIONr_mcbond_it1.021.51149
X-RAY DIFFRACTIONr_mcangle_it1.74121856
X-RAY DIFFRACTIONr_scbond_it2.2413659
X-RAY DIFFRACTIONr_scangle_it3.914.5592
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 35 -
Rwork0.303 644 -
all-679 -
obs--98.55 %

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