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- PDB-3lba: The Crystal Structure of smu.1229 from Streptococcus mutans UA159... -

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Basic information

Entry
Database: PDB / ID: 3lba
TitleThe Crystal Structure of smu.1229 from Streptococcus mutans UA159 bound to hypoxanthine
ComponentsPutative purine nucleoside phosphorylase
KeywordsTRANSFERASE / punA / Glycosyltransferase
Function / homology
Function and homology information


nucleoside metabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / cytoplasm
Similarity search - Function
Purine nucleoside phosphorylase I, inosine/guanosine-specific / Purine nucleoside phosphorylase / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HYPOXANTHINE / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsSu, X.-D. / Hou, Q.M. / Wang, H.F. / Liu, X.
CitationJournal: TO BE PUBLISHED
Title: The Crystal Structure of smu.1229 from Streptococcus mutans UA159 bound to hypoxanthine
Authors: Su, X.-D. / Hou, Q.M. / Wang, H.F. / Liu, X.
History
DepositionJan 8, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Putative purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6643
Polymers32,4321
Non-polymers2322
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.500, 83.500, 127.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Putative purine nucleoside phosphorylase / smu.1229


Mass: 32431.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: smu.1229 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8DTU4, purine-nucleoside phosphorylase
#2: Chemical ChemComp-HPA / HYPOXANTHINE


Mass: 136.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% (w/v) PEG 3350, 0.15M ammonium sulfate, 0.1M bis-tris, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.24→63 Å / Num. all: 15986 / Num. obs: 15986 / % possible obs: 100 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 34.6 Å2
Reflection shellResolution: 2.24→2.36 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.5.0066refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→34.79 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.899 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.908 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24639 798 5 %RANDOM
Rwork0.19688 ---
obs0.1993 15178 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 67.1 Å2 / Biso mean: 34.225 Å2 / Biso min: 13.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20.35 Å20 Å2
2--0.7 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 2.24→34.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1955 0 15 51 2021
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222007
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0381.9882714
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4555257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.88224.93779
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.81615336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.131157
X-RAY DIFFRACTIONr_chiral_restr0.120.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211483
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0281.51275
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.77422030
X-RAY DIFFRACTIONr_scbond_it2.9253732
X-RAY DIFFRACTIONr_scangle_it4.4014.5684
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.24→2.298 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 69 -
Rwork0.233 1120 -
all-1189 -
obs--99.92 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramtop.txt
X-RAY DIFFRACTION4param.txtion.top

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