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

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Basic information

Entry
Database: PDB / ID: 4dan
TitleCrystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis in complex with 2-fluoroadenosine
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-2FA / Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.56 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)55,6954
Polymers55,1242
Non-polymers5702
Water00
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)167,08412
Polymers165,3736
Non-polymers1,7116
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
Buried area24710 Å2
ΔGint-111 kcal/mol
Surface area45420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.804, 135.804, 55.154
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 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: O34925, purine-nucleoside phosphorylase
#2: Chemical ChemComp-2FA / 2-(6-AMINO-2-FLUORO-PURIN-9-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL / 2-FLUOROADENOSINE


Mass: 285.232 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12FN5O4
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: 2.66 Å3/Da / Density % sol: 53.82 %
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, L10.508
11h+k,-k,-l20.492
ReflectionResolution: 2.56→40 Å / Num. all: 17770 / Num. obs: 17770 / % possible obs: 93.7 % / Redundancy: 4.4 % / Rsym value: 0.104 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.56-2.74.40.3032.11132825610.30393.7
2.7-2.864.40.2242.81081024320.22493.6
2.86-3.064.50.16341023022910.16393.4
3.06-3.34.50.1255.4957321390.12594.1
3.3-3.624.50.0967.1872119520.09693.5
3.62-4.054.50.0828.3806417970.08294.1
4.05-4.674.50.0699.9710315860.06994.1
4.67-5.724.40.087.7600313500.0894.1
5.72-8.14.40.0828470610700.08293.8
8.1-34.6114.10.0589.924185920.05893

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.56→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.883 / WRfactor Rfree: 0.2088 / WRfactor Rwork: 0.1565 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8382 / SU B: 9.56 / SU ML: 0.198 / SU R Cruickshank DPI: 0.1036 / SU Rfree: 0.0548 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.211 943 5.3 %RANDOM
Rwork0.1566 ---
obs0.1596 17733 92.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 53.26 Å2 / Biso mean: 23.5882 Å2 / Biso min: 8.8 Å2
Baniso -1Baniso -2Baniso -3
1--12.58 Å20 Å20 Å2
2---12.58 Å20 Å2
3---25.16 Å2
Refinement stepCycle: LAST / Resolution: 2.56→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3509 0 40 0 3549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223607
X-RAY DIFFRACTIONr_bond_other_d0.0060.022349
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.9744888
X-RAY DIFFRACTIONr_angle_other_deg0.88835768
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8365458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95824.868152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.89615616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1611516
X-RAY DIFFRACTIONr_chiral_restr0.0710.2573
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024016
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02702
X-RAY DIFFRACTIONr_mcbond_it0.5881.52270
X-RAY DIFFRACTIONr_mcbond_other0.0951.5946
X-RAY DIFFRACTIONr_mcangle_it1.11723659
X-RAY DIFFRACTIONr_scbond_it1.58431337
X-RAY DIFFRACTIONr_scangle_it2.624.51229
LS refinement shellResolution: 2.56→2.624 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 64 -
Rwork0.199 1175 -
all-1239 -
obs--89.14 %

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