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

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Basic information

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


uridine catabolic process / uridine phosphorylase activity / 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
Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 / 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)26,0775
Polymers25,7001
Non-polymers3764
Water3,279182
1
A: Purine nucleoside phosphorylase deoD-type
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)156,46030
Polymers154,2026
Non-polymers2,25824
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 area26500 Å2
ΔGint-403 kcal/mol
Surface area42280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.000, 122.000, 68.000
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-417-

HOH

21A-420-

HOH

31A-421-

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-SO4 / SULFATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.84 Å3/Da / Density % sol: 56.72 %
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: 0.9758 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9758 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 58855 / Num. obs: 58855 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.053 / Χ2: 1.019 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.4-1.4550.4757910.7711100
1.45-1.515.10.31758100.8231100
1.51-1.585.20.21457990.8631100
1.58-1.665.20.15658350.911100
1.66-1.765.20.11658331.0271100
1.76-1.95.20.07758581.081100
1.9-2.095.20.05858831.17199.9
2.09-2.395.20.05659211.354199.9
2.39-3.025.10.05359721.089199.9
3.02-504.90.03561531.081197.9

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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: 1.4→39.934 Å / Occupancy max: 1 / Occupancy min: 0.24 / FOM work R set: 0.928 / SU ML: 0.27 / σ(F): 1 / Phase error: 12.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1643 2810 4.94 %RANDOM
Rwork0.1489 ---
obs0.1496 56903 96.61 %-
all-58855 --
Solvent computationShrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.444 Å2 / ksol: 0.504 e/Å3
Displacement parametersBiso max: 92.15 Å2 / Biso mean: 20.6062 Å2 / Biso min: 7.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.1479 Å2-0 Å2-0 Å2
2--0.1479 Å2-0 Å2
3----0.2957 Å2
Refinement stepCycle: LAST / Resolution: 1.4→39.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 22 182 1935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091996
X-RAY DIFFRACTIONf_angle_d1.2822724
X-RAY DIFFRACTIONf_chiral_restr0.07313
X-RAY DIFFRACTIONf_plane_restr0.006356
X-RAY DIFFRACTIONf_dihedral_angle_d13.314743
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.42420.2461300.22332412254288
1.4242-1.45010.22991400.19332505264591
1.4501-1.4780.20331440.17582533267793
1.478-1.50810.1691390.15792584272394
1.5081-1.54090.15921360.14382630276696
1.5409-1.57680.17881370.14962650278796
1.5768-1.61620.16271450.14672648279396
1.6162-1.65990.14311400.13432682282297
1.6599-1.70880.15211430.13412671281497
1.7088-1.76390.15031390.13452717285698
1.7639-1.8270.1251290.12692744287398
1.827-1.90010.13691410.12692728286998
1.9001-1.98660.1371350.11972766290199
1.9866-2.09130.14921250.12772784290999
2.0913-2.22230.15731320.12632807293999
2.2223-2.39390.12441540.1252783293799
2.3939-2.63480.14871450.13482821296699
2.6348-3.01590.1721340.149628462980100
3.0159-3.79920.16991530.153128933046100
3.7992-39.95010.19731690.18932889305895
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3475-0.2135-0.03510.3876-0.0220.4103-0.0081-0.0855-0.07940.00950.0470.10670.0711-0.08610.01970.1126-0.0233-0.00370.10250.03630.113336.16459.060558.3335
20.22130.04520.12620.23090.01830.07030.03990.0493-0.1125-0.09660.0567-0.0793-0.02690.143200.1625-0.010.00750.1403-0.01720.141349.08468.651143.6062
30.59330.0213-0.05570.14830.09820.37840.01640.0437-0.0444-0.0422-0.01680.0010.0207-0.04450.00010.11810.00070.00010.0762-0.00810.096954.235214.384647.8521
40.19140.108-0.03630.11340.01770.0253-0.08670.138-0.0929-0.08420.02280.0496-0.04920.0256-0.00080.1739-0.0268-0.02980.1533-0.01690.114546.1869.90541.3209
50.1564-0.09730.0050.1249-00.12880.05670.1171-0.3516-0.13-0.09840.05830.03340.102-0.01030.164-0.02050.0120.1101-0.00230.113143.2311-0.766448.2695
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:80)A2 - 80
2X-RAY DIFFRACTION2chain 'A' and (resseq 81:102)A81 - 102
3X-RAY DIFFRACTION3chain 'A' and (resseq 103:192)A103 - 192
4X-RAY DIFFRACTION4chain 'A' and (resseq 193:217)A193 - 217
5X-RAY DIFFRACTION5chain 'A' and (resseq 218:234)A218 - 234

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