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- PDB-3uaz: Crystal structure of Bacillus cereus adenosine phosphorylase D204... -

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Basic information

Entry
Database: PDB / ID: 3uaz
TitleCrystal structure of Bacillus cereus adenosine phosphorylase D204N mutant 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: 1.4 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 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / 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)26,2485
Polymers25,6991
Non-polymers5484
Water3,513195
1
A: Purine nucleoside phosphorylase deoD-type
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)157,48730
Polymers154,1966
Non-polymers3,29124
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 area28310 Å2
ΔGint-276 kcal/mol
Surface area42090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.700, 122.700, 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-429-

HOH

21A-431-

HOH

31A-433-

HOH

41A-434-

HOH

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Components

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


Mass: 25699.389 Da / Num. of mol.: 1 / Fragment: Adenosine phosphorylase / Mutation: D204N
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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.87 Å3/Da / Density % sol: 57.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.1 - 1.25 M sodium citrate, 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: 8-BM / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. all: 59410 / Num. obs: 59410 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Rmerge(I) obs: 0.077 / Χ2: 1.97 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.4-1.4580.52658581.4561100
1.45-1.518.20.38558771.6111100
1.51-1.588.20.29758701.7971100
1.58-1.668.30.23258641.9521100
1.66-1.768.30.18758872.2431100
1.76-1.98.30.14559172.3411100
1.9-2.098.30.11659412.4041100
2.09-2.398.20.10159782.581100
2.39-3.018.10.06860421.7781100
3.01-207.80.03861761.483197.7

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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→19.812 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9355 / SU ML: 0.26 / σ(F): 1 / Phase error: 12.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1547 2833 4.94 %RANDOM
Rwork0.1403 ---
obs0.141 57352 96.33 %-
all-59410 --
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.281 Å2 / ksol: 0.479 e/Å3
Displacement parametersBiso max: 83.82 Å2 / Biso mean: 17.8294 Å2 / Biso min: 5.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.5284 Å20 Å2-0 Å2
2--0.5284 Å2-0 Å2
3----1.0567 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.812 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 36 195 1986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092128
X-RAY DIFFRACTIONf_angle_d1.3162921
X-RAY DIFFRACTIONf_chiral_restr0.074352
X-RAY DIFFRACTIONf_plane_restr0.006375
X-RAY DIFFRACTIONf_dihedral_angle_d16.363781
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 (%)
1.4-1.42420.22471330.19872526265991
1.4242-1.45010.21911380.18542566270492
1.4501-1.4780.16841420.16622575271792
1.478-1.50810.15991420.15442603274594
1.5081-1.54090.16981420.14352623276595
1.5409-1.57670.14281320.13982670280295
1.5767-1.61610.16491400.13512672281296
1.6161-1.65980.1381480.13022673282196
1.6598-1.70860.14071350.12362720285597
1.7086-1.76370.13331570.12772679283697
1.7637-1.82670.14091330.12942741287497
1.8267-1.89980.15231380.12792763290198
1.8998-1.98620.12041380.12432777291598
1.9862-2.09080.16991310.12682801293299
2.0908-2.22170.17071310.12462808293999
2.2217-2.39290.14081590.12462787294698
2.3929-2.63320.14631450.13412828297399
2.6332-3.01310.14161340.14292875300999
3.0131-3.79190.15321520.14172905305799
3.7919-19.81370.17031630.16232927309095
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)
10.288-0.1904-0.02260.38730.02380.2486-0.0055-0.067-0.10880.00060.04370.15020.032-0.09350.03610.1085-0.02020.00630.11850.02840.154233.99467.032857.6826
20.10.00430.01370.0240.03540.1045-0.0528-0.0704-0.0959-0.12030.0012-0.03480.1417-0.02640.0010.0853-0.01150.01970.0640.03690.088738.57524.339157.4514
30.2334-0.0380.21330.6143-0.09550.17730.0228-0.0007-0.0449-0.03580.01650.0068-0.02460.01160.04120.0852-0.00410.00580.0860.00060.087246.241712.317752.0035
40.3006-0.07220.03210.0405-0.02160.02580.01590.00650.0387-0.0088-0.0321-0.04430.001-0.0246-00.0987-0.00510.00490.0871-0.0080.101555.357817.884350.3032
50.3002-0.0470.01550.1551-0.06040.1295-0.01710.0374-0.0477-0.02350.07590.04150.04850.04510.02110.11660.00340.00260.0774-0.00040.110257.21977.729753.2373
60.1711-0.03730.0040.1341-0.23240.3380.0610.0869-0.0117-0.0928-0.0727-0.06810.084-0.01370.01080.1060.00860.0020.0907-0.01560.089250.896416.992540.7431
70.2138-0.01030.11690.09080.01190.06990.02620.1475-0.0291-0.0132-0.06650.0055-0.0376-0.0404-0.03310.10030.02050.00170.1025-0.00210.080856.080719.602939.4526
80.47270.3453-0.0820.5566-0.22460.1459-0.05390.0941-0.0535-0.10160.08290.0877-0.02670.05910.00830.1152-0.0099-0.01180.1017-0.0090.085148.913812.58646.1684
90.4317-0.0155-0.00490.24820.00210.06980.00930.2588-0.3279-0.2612-0.11630.1905-0.04060.0441-0.01430.0952-0.01290.00760.0495-0.00080.11643.1106-0.298547.471
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:52)A2 - 52
2X-RAY DIFFRACTION2chain 'A' and (resseq 53:65)A53 - 65
3X-RAY DIFFRACTION3chain 'A' and (resseq 66:102)A66 - 102
4X-RAY DIFFRACTION4chain 'A' and (resseq 103:119)A103 - 119
5X-RAY DIFFRACTION5chain 'A' and (resseq 120:144)A120 - 144
6X-RAY DIFFRACTION6chain 'A' and (resseq 145:164)A145 - 164
7X-RAY DIFFRACTION7chain 'A' and (resseq 165:181)A165 - 181
8X-RAY DIFFRACTION8chain 'A' and (resseq 182:214)A182 - 214
9X-RAY DIFFRACTION9chain 'A' and (resseq 215:234)A215 - 234

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