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- PDB-1xe3: Crystal Structure of purine nucleoside phosphorylase DeoD from Ba... -

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Basic information

Entry
Database: PDB / ID: 1xe3
TitleCrystal Structure of purine nucleoside phosphorylase DeoD from Bacillus anthracis
Componentspurine nucleoside phosphorylase
KeywordsTRANSFERASE / PURINE NUCLEOSIDE PHOSPHORYLASE / DeoD / SPINE / Structural Genomics / Structural Proteomics in Europe
Function / homology
Function and homology information


purine nucleoside metabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity
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 anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsGrenha, R. / Levdikov, V.M. / Fogg, M. / Blagova, E.V. / Brannigan, J.A. / Wilkinson, A.J. / Wilson, K.S. / Structural Proteomics in Europe (SPINE)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Structure of purine nucleoside phosphorylase (DeoD) from Bacillus anthracis.
Authors: Grenha, R. / Levdikov, V.M. / Fogg, M.J. / Blagova, E.V. / Brannigan, J.A. / Wilkinson, A.J. / Wilson, K.S.
History
DepositionSep 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_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
B: purine nucleoside phosphorylase
C: purine nucleoside phosphorylase
D: purine nucleoside phosphorylase
E: purine nucleoside phosphorylase
F: purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,56312
Polymers161,3506
Non-polymers2136
Water12,899716
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19820 Å2
ΔGint-189 kcal/mol
Surface area46640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.861, 128.257, 223.565
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a hexamer.

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Components

#1: Protein
purine nucleoside phosphorylase


Mass: 26891.666 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: deoD / Plasmid: pET-YSBLIC / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: Q81T09, purine-nucleoside phosphorylase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 716 / 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: 3 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 400, magnesium chloride, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54189 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 23, 2004 / Details: osmic multilayer mirrors
RadiationMonochromator: multilayer mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54189 Å / Relative weight: 1
ReflectionResolution: 2.24→20 Å / Num. all: 81257 / Num. obs: 81257 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.141
Reflection shellResolution: 2.24→2.32 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 1.84 / Num. unique all: 7218 / % possible all: 82

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ECP

1ecp


Resolution: 2.24→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.717 / SU ML: 0.141 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.25 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23523 4065 5 %RANDOM
Rwork0.18097 ---
all0.18369 81055 --
obs0.18369 81055 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.373 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 2.24→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10728 0 6 716 11450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02210888
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210081
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.96514729
X-RAY DIFFRACTIONr_angle_other_deg0.963323402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.80751398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.89424.627456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.661151910
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3941555
X-RAY DIFFRACTIONr_chiral_restr0.1080.21738
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212132
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022139
X-RAY DIFFRACTIONr_nbd_refined0.1920.22241
X-RAY DIFFRACTIONr_nbd_other0.1910.210767
X-RAY DIFFRACTIONr_nbtor_refined0.1740.25228
X-RAY DIFFRACTIONr_nbtor_other0.0890.26349
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2709
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3170.294
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.239
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.751.58907
X-RAY DIFFRACTIONr_mcbond_other0.1131.52907
X-RAY DIFFRACTIONr_mcangle_it0.907211149
X-RAY DIFFRACTIONr_scbond_it1.68534550
X-RAY DIFFRACTIONr_scangle_it2.5674.53579
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.24→2.297 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 241 -
Rwork0.239 5002 -
obs--100 %

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