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- PDB-4d8v: Crystal structure of the hexameric purine nucleoside phosphorylas... -

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Basic information

Entry
Database: PDB / ID: 4d8v
TitleCrystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis at pH 4.2
ComponentsPurine nucleoside phosphorylase deoD-type
KeywordsTRANSFERASE / Phosphorylase/hydrolase-like
Function / homology
Function and homology information


purine-nucleoside phosphorylase / purine nucleoside catabolic process / purine-nucleoside phosphorylase activity / 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: 2.35 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 / 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)55,7798
Polymers55,1242
Non-polymers6556
Water1,802100
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)167,33624
Polymers165,3736
Non-polymers1,96418
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 area26300 Å2
ΔGint-298 kcal/mol
Surface area45020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.827, 136.827, 57.108
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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 / Production host: Escherichia coli (E. coli)
References: UniProt: O34925, purine-nucleoside phosphorylase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 4.2
Details: 0.1 M sodium phosphate, 2 M ammonium sulfate, pH 4.2, 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: 2.35→40 Å / Num. obs: 25344 / % possible obs: 98.3 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.092 / Χ2: 1.025 / Net I/σ(I): 15.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.35-2.437.60.48824781.047197.4
2.43-2.538.20.42825421.031199.6
2.53-2.658.30.3625561.0591100
2.65-2.798.20.25925511.0071100
2.79-2.968.10.19425751.0371100
2.96-3.197.80.14325571.006199.9
3.19-3.517.30.11525711.023199.9
3.51-4.024.60.122241.02186.2
4.02-5.067.40.07826081.009199.7
5.06-408.40.05126821.007199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.904 / WRfactor Rfree: 0.2955 / WRfactor Rwork: 0.2436 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7816 / SU B: 7.045 / SU ML: 0.173 / SU R Cruickshank DPI: 0.3458 / SU Rfree: 0.2613 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.346 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1283 5.1 %RANDOM
Rwork0.225 ---
obs0.2275 25014 96.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 89.66 Å2 / Biso mean: 49.4395 Å2 / Biso min: 30.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.01 Å20 Å2
2---0.03 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3522 0 40 100 3662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223618
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.9714901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3175462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81624.868152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52815619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8751516
X-RAY DIFFRACTIONr_chiral_restr0.0880.2569
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022676
X-RAY DIFFRACTIONr_mcbond_it0.7271.52283
X-RAY DIFFRACTIONr_mcangle_it1.39523682
X-RAY DIFFRACTIONr_scbond_it2.13131335
X-RAY DIFFRACTIONr_scangle_it3.5914.51218
LS refinement shellResolution: 2.35→2.405 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 85 -
Rwork0.276 1475 -
all-1560 -
obs--83.02 %

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