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

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Basic information

Entry
Database: PDB / ID: 3uaw
TitleCrystal structure of adenosine phosphorylase from Bacillus cereus complexed with adenosine
ComponentsPurine nucleoside phosphorylase deoD-type
KeywordsTRANSFERASE / Necleoside phosphorylase I (NP-I) family
Function / homology
Function and homology information


purine nucleoside metabolic process / nucleoside catabolic process / purine-nucleoside phosphorylase activity / purine-nucleoside phosphorylase
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
ADENOSINE / 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)26,3446
Polymers25,7001
Non-polymers6445
Water3,675204
1
A: Purine nucleoside phosphorylase deoD-type
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)158,06436
Polymers154,2026
Non-polymers3,86130
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 area30080 Å2
ΔGint-390 kcal/mol
Surface area39780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.000, 121.000, 67.100
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-416-

HOH

21A-439-

HOH

31A-443-

HOH

41A-444-

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-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.76 Å3/Da / Density % sol: 55.41 %
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: 22-ID / Wavelength: 0.99997 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. all: 88363 / Num. obs: 88363 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 13.1 % / Rmerge(I) obs: 0.052 / Χ2: 1.07 / Net I/σ(I): 13
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.2-1.245.40.54679490.91189.3
1.24-1.2910.40.44888840.912199.8
1.29-1.3513.30.35488980.927199.8
1.35-1.42140.26489160.927199.8
1.42-1.5114.30.16788870.946199.7
1.51-1.6314.50.11289530.986199.6
1.63-1.7914.60.07889301.093199.3
1.79-2.0514.70.07189391.239198.8
2.05-2.5914.80.0689521.444197.9
2.59-5014.40.02490551.121195.1

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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→26.669 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.9477 / SU ML: 0.28 / σ(F): 1 / Phase error: 10.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.141 4165 4.96 %RANDOM
Rwork0.1251 ---
obs0.1259 83888 92.87 %-
all-88363 --
Solvent computationShrinkage radii: 0.05 Å / VDW probe radii: 0.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.507 Å2 / ksol: 0.501 e/Å3
Displacement parametersBiso max: 46.37 Å2 / Biso mean: 15.3875 Å2 / Biso min: 5.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.3579 Å2-0 Å2-0 Å2
2--0.3579 Å2-0 Å2
3----0.7159 Å2
Refinement stepCycle: LAST / Resolution: 1.2→26.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1747 0 41 204 1992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132215
X-RAY DIFFRACTIONf_angle_d1.3483037
X-RAY DIFFRACTIONf_chiral_restr0.081360
X-RAY DIFFRACTIONf_plane_restr0.006393
X-RAY DIFFRACTIONf_dihedral_angle_d13.928806
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 (%)
1.199-1.21270.2723880.26571720180861
1.2127-1.22690.26351190.23472242236180
1.2269-1.24190.2231320.20412442257487
1.2419-1.25760.1871230.17012543266689
1.2576-1.27420.16491340.1442522265690
1.2742-1.29160.15051390.11992585272491
1.2916-1.31010.13931410.11032619276093
1.3101-1.32960.14221360.09962634277093
1.3296-1.35040.11911480.09932618276693
1.3504-1.37250.13071410.10112634277594
1.3725-1.39620.11341440.09772679282394
1.3962-1.42160.12411370.0982672280994
1.4216-1.44890.12931430.09492678282195
1.4489-1.47850.12821520.08872692284495
1.4785-1.51060.11071390.09012723286296
1.5106-1.54580.10411280.08952730285895
1.5458-1.58440.10571540.08692728288297
1.5844-1.62730.09751490.08812744289396
1.6273-1.67510.11771490.08932720286996
1.6751-1.72920.11111410.0942769291096
1.7292-1.7910.11091390.09122747288696
1.791-1.86270.11581420.0962757289996
1.8627-1.94740.1211350.0972785292097
1.9474-2.05010.11031360.10212766290296
2.0501-2.17850.13351290.10212812294197
2.1785-2.34660.12681520.11322799295197
2.3466-2.58250.13841480.12362796294496
2.5825-2.95580.17131300.14632835296596
2.9558-3.72240.14651480.14722849299796
3.7224-26.67570.17841690.18162883305293

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