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- PDB-3odg: crystal structure of xanthosine phosphorylase bound with xanthine... -

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Basic information

Entry
Database: PDB / ID: 3odg
Titlecrystal structure of xanthosine phosphorylase bound with xanthine from Yersinia pseudotuberculosis
ComponentsXanthosine phosphorylase
KeywordsTRANSFERASE / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / Purine Nucleoside Phosphorylase / purine nucleoside binding
Function / homology
Function and homology information


nucleoside metabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / cytoplasm
Similarity search - Function
Xanthosine phosphorylase / 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
XANTHINE / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesYersinia pseudotuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsKim, J. / Ramagopal, U.A. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: crystal structure of xanthosine phosphorylase bound with xanthine from Yersinia pseudotuberculosis
Authors: Kim, J. / Ramagopal, U.A. / Almo, S.C.
History
DepositionAug 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Derived calculations / Structure summary / Category: audit_author / struct_site
Item: _audit_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id ..._audit_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xanthosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1313
Polymers30,9431
Non-polymers1882
Water4,540252
1
A: Xanthosine phosphorylase
hetero molecules

A: Xanthosine phosphorylase
hetero molecules

A: Xanthosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3929
Polymers92,8293
Non-polymers5636
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area7360 Å2
ΔGint-67 kcal/mol
Surface area29860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.470, 96.470, 48.906
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Xanthosine phosphorylase


Mass: 30942.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Gene: pndA, xapA, YPTB1201 / Plasmid: LIC-PET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q66D48, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-XAN / XANTHINE


Mass: 152.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.12 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl PH 8.5, 0.2M Sodium Acetate, 30% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 9, 2009
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.64→48.24 Å / Num. all: 31965 / Num. obs: 31056 / % possible obs: 97.2 % / Redundancy: 11.7 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.076 / Net I/σ(I): 24.7
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2550 / Rsym value: 0.483 / % possible all: 81.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREP10.2.23phasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YQQ

1yqq


Resolution: 1.64→48.24 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.259 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18727 1560 5 %RANDOM
Rwork0.15518 ---
obs0.15689 29504 97.02 %-
all-30354 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.427 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0.03 Å20 Å2
2---0.07 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.64→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 12 252 2323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222125
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.9882881
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6135274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.55124.68479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53415358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.618157
X-RAY DIFFRACTIONr_chiral_restr0.1110.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211585
X-RAY DIFFRACTIONr_mcbond_it0.9911.51362
X-RAY DIFFRACTIONr_mcangle_it1.70322202
X-RAY DIFFRACTIONr_scbond_it2.8593763
X-RAY DIFFRACTIONr_scangle_it4.7794.5679
LS refinement shellResolution: 1.639→1.682 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 91 -
Rwork0.235 1711 -
obs--76.98 %
Refinement TLS params.Method: refined / Origin x: -28.102 Å / Origin y: -19.958 Å / Origin z: -0.107 Å
111213212223313233
T0.0046 Å20.0028 Å20.0009 Å2-0.0117 Å2-0.0144 Å2--0.3068 Å2
L0.8557 °2-0.0526 °2-0.0176 °2-0.8319 °20.1633 °2--0.3095 °2
S-0.0122 Å °-0.026 Å °0.0671 Å °0.033 Å °0.0464 Å °-0.1531 Å °0.0044 Å °0.0477 Å °-0.0342 Å °

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