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

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Basic information

Entry
Database: PDB / ID: 4dar
TitleCrystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis in complex with tubercidin
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
Chem-TBN / Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.15 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8282
Polymers27,5621
Non-polymers2661
Water00
1
A: Purine nucleoside phosphorylase deoD-type
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)166,97012
Polymers165,3736
Non-polymers1,5986
Water0
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 area24320 Å2
ΔGint-97 kcal/mol
Surface area46360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.638, 135.638, 57.560
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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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: Chemical ChemComp-TBN / '2-(4-AMINO-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL / 7-DEAZAADENOSINE


Mass: 266.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14N4O4
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: 2.77 Å3/Da / Density % sol: 55.64 %
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: 3.15→117.466 Å / Num. all: 5743 / Num. obs: 5743 / % possible obs: 99.8 % / Redundancy: 5.3 % / Rsym value: 0.116 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.15-3.325.40.34243928120.34100
3.32-3.525.40.242.741937710.24100
3.52-3.765.40.1743.839557320.174100
3.76-4.075.40.123536766870.123100
4.07-4.455.30.0966.433786350.096100
4.45-4.985.30.0916.630245710.09199.9
4.98-5.755.30.1264.827405210.12699.8
5.75-7.045.20.1175.523144450.11799.8
7.04-9.9650.0698.317723560.06999.1
9.96-39.1554.30.0718.19062130.07196.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→20 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.879 / WRfactor Rfree: 0.2818 / WRfactor Rwork: 0.2241 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8007 / SU B: 50.416 / SU ML: 0.402 / SU Rfree: 0.4967 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.497 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2714 260 4.6 %RANDOM
Rwork0.2168 ---
obs0.2193 5713 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 87.58 Å2 / Biso mean: 60.804 Å2 / Biso min: 41.33 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å2-0.76 Å20 Å2
2---1.52 Å20 Å2
3---2.28 Å2
Refinement stepCycle: LAST / Resolution: 3.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1761 0 19 0 1780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221809
X-RAY DIFFRACTIONr_bond_other_d0.0010.021181
X-RAY DIFFRACTIONr_angle_refined_deg1.1531.9732451
X-RAY DIFFRACTIONr_angle_other_deg0.85632898
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9565230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95624.86876
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75815309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.234158
X-RAY DIFFRACTIONr_chiral_restr0.0560.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022014
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02354
X-RAY DIFFRACTIONr_mcbond_it0.5011.51140
X-RAY DIFFRACTIONr_mcbond_other0.041.5475
X-RAY DIFFRACTIONr_mcangle_it0.93121838
X-RAY DIFFRACTIONr_scbond_it0.7763669
X-RAY DIFFRACTIONr_scangle_it1.4364.5613
LS refinement shellResolution: 3.15→3.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 12 -
Rwork0.258 402 -
all-414 -
obs--100 %

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