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- PDB-3uax: Crystal structure of adenosine phosphorylase from Bacillus cereus... -

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Basic information

Entry
Database: PDB / ID: 3uax
TitleCrystal structure of adenosine phosphorylase from Bacillus cereus complexed with inosine
ComponentsPurine nucleoside phosphorylase deoD-type
KeywordsTRANSFERASE / Necleoside phosphorylase I (NP-I) family
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
INOSINE / Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsDessanti, P. / Zhang, Y. / Allegrini, S. / Tozzi, M.G. / Sgarrella, F. / Ealick, S.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structural basis of the substrate specificity of Bacillus cereus adenosine phosphorylase.
Authors: Dessanti, P. / Zhang, Y. / Allegrini, S. / Tozzi, M.G. / Sgarrella, F. / Ealick, S.E.
History
DepositionOct 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)26,1574
Polymers25,7001
Non-polymers4563
Water3,927218
1
A: Purine nucleoside phosphorylase deoD-type
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)156,94124
Polymers154,2026
Non-polymers2,73818
Water1086
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_666-y+1,-x+1,-z+3/21
crystal symmetry operation11_656-x+y+1,y,-z+3/21
crystal symmetry operation12_556x,x-y,-z+3/21
Buried area27160 Å2
ΔGint-262 kcal/mol
Surface area42300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.800, 122.800, 68.100
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-452-

HOH

21A-453-

HOH

31A-454-

HOH

41A-455-

HOH

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Components

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


Mass: 25700.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: deoD / Plasmid: pET5b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5EEL8, purine-nucleoside phosphorylase
#2: Chemical ChemComp-NOS / INOSINE


Mass: 268.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N4O5
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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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: 2.88 Å3/Da / Density % sol: 57.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.3-1.5 M ammonium sulfate, pH 5.5, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. all: 88185 / Num. obs: 88185 / % possible obs: 93.5 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.06 / Χ2: 1.271 / Net I/σ(I): 21.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.2-1.2420.35772171.025177.8
1.24-1.292.10.28578631.052184.4
1.29-1.352.30.21382621.122188.7
1.35-1.422.50.1786021.222192.2
1.42-1.512.90.1389341.411195.6
1.51-1.633.50.10392101.401198.4
1.63-1.793.80.07993951.328199.7
1.79-2.0540.06394421.315199.9
2.05-2.594.20.06495291.411199.8
2.59-505.40.05397311.117197.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ECP

1ecp


Resolution: 1.2→32.428 Å / Occupancy max: 1 / Occupancy min: 0.06 / FOM work R set: 0.9377 / SU ML: 0.22 / σ(F): 1 / Phase error: 11.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1477 4188 4.98 %RANDOM
Rwork0.1277 ---
obs0.1286 84174 89.4 %-
all-88185 --
Solvent computationShrinkage radii: 0.05 Å / VDW probe radii: 0.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.9 Å2 / ksol: 0.478 e/Å3
Displacement parametersBiso max: 48.21 Å2 / Biso mean: 15.5028 Å2 / Biso min: 6.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.4979 Å2-0 Å2-0 Å2
2--0.4979 Å2-0 Å2
3----0.9959 Å2
Refinement stepCycle: LAST / Resolution: 1.2→32.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1699 0 30 218 1947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082121
X-RAY DIFFRACTIONf_angle_d1.2922921
X-RAY DIFFRACTIONf_chiral_restr0.076354
X-RAY DIFFRACTIONf_plane_restr0.006378
X-RAY DIFFRACTIONf_dihedral_angle_d16.359782
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.21360.2421970.21621927202465
1.2136-1.22790.21461020.19631983208568
1.2279-1.24290.21061100.18932058216870
1.2429-1.25860.15771160.17512111222772
1.2586-1.27520.16591150.16432210232575
1.2752-1.29270.19491190.15862289240878
1.2927-1.31110.16961450.1432325247080
1.3111-1.33070.15611470.13172394254182
1.3307-1.35150.1441170.12772440255782
1.3515-1.37370.14341200.12492509262985
1.3737-1.39730.14431400.12692564270487
1.3973-1.42280.16361280.11432622275088
1.4228-1.45010.1611420.11212641278389
1.4501-1.47970.14391470.10342691283891
1.4797-1.51190.11741600.10072760292094
1.5119-1.54710.12671370.09372793293094
1.5471-1.58570.12621520.09152865301797
1.5857-1.62860.10241560.08622890304698
1.6286-1.67650.11571550.09092908306398
1.6765-1.73070.1031580.09332928308698
1.7307-1.79250.11781520.09742953310599
1.7925-1.86430.12151480.09692936308499
1.8643-1.94910.13841400.10372997313799
1.9491-2.05180.12211470.10662960310799
2.0518-2.18040.14951470.1092996314399
2.1804-2.34870.12141520.11330223174100
2.3487-2.58490.1321680.12312992316099
2.5849-2.95880.16441310.14013069320099
2.9588-3.72690.15341660.148730853251100
3.7269-32.44020.19081740.17193068324294

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