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

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Basic information

Entry
Database: PDB / ID: 4dao
TitleCrystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis in complex with adenine
ComponentsPurine nucleoside phosphorylase deoD-type
KeywordsTRANSFERASE / Phosphorylase/hydrolase-like
Function / homology
Function and homology information


purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / purine nucleoside catabolic process / 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
ADENINE / Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.22 Å
AuthorsGiuseppe, P.O. / Martins, N.H. / Meza, A.N. / 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 13, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4875
Polymers55,1242
Non-polymers3623
Water86548
1
A: Purine nucleoside phosphorylase deoD-type
B: Purine nucleoside phosphorylase deoD-type
hetero molecules

A: Purine nucleoside phosphorylase deoD-type
B: Purine nucleoside phosphorylase deoD-type
hetero molecules

A: Purine nucleoside phosphorylase deoD-type
B: Purine nucleoside phosphorylase deoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,46015
Polymers165,3736
Non-polymers1,0879
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
Buried area21560 Å2
ΔGint-115 kcal/mol
Surface area46830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.458, 136.458, 55.484
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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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.: 2
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: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.71 Å3/Da / Density % sol: 54.53 %
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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.5
11h+k,-k,-l20.5
ReflectionResolution: 2.22→40 Å / Num. obs: 29480 / % possible obs: 99.8 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.044 / Χ2: 1.005 / Net I/σ(I): 18.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.22-2.35.20.28528571.004198.3
2.3-2.395.40.22829151.008199.8
2.39-2.55.60.18129311.0061100
2.5-2.635.60.15529401.0071100
2.63-2.85.70.1129281.0051100
2.8-3.015.70.09129301.0011100
3.01-3.325.70.06529731.0031100
3.32-3.85.70.036294311100
3.8-4.785.70.02429891.0061100
4.78-405.50.02630741.007199.6

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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: 2.22→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.2067 / WRfactor Rwork: 0.1443 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8508 / SU B: 7.099 / SU ML: 0.15 / SU R Cruickshank DPI: 0.0365 / SU Rfree: 0.0357 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2077 1480 5 %RANDOM
Rwork0.1482 ---
obs0.1512 29441 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 71.61 Å2 / Biso mean: 40.3613 Å2 / Biso min: 20.43 Å2
Baniso -1Baniso -2Baniso -3
1--10.76 Å20 Å20 Å2
2---10.76 Å20 Å2
3---21.52 Å2
Refinement stepCycle: LAST / Resolution: 2.22→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3510 0 26 48 3584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223602
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.9674877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5635462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37924.902153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.68315619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2831516
X-RAY DIFFRACTIONr_chiral_restr0.1030.2568
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022676
X-RAY DIFFRACTIONr_mcbond_it0.8631.52276
X-RAY DIFFRACTIONr_mcangle_it1.60323672
X-RAY DIFFRACTIONr_scbond_it2.44231326
X-RAY DIFFRACTIONr_scangle_it3.9744.51203
LS refinement shellResolution: 2.22→2.277 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 96 -
Rwork0.21 1939 -
all-2035 -
obs--96.22 %

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