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- PDB-1a9s: BOVINE PURINE NUCLEOSIDE PHOSPHORYLASE COMPLEXED WITH INOSINE AND... -

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Basic information

Entry
Database: PDB / ID: 1a9s
TitleBOVINE PURINE NUCLEOSIDE PHOSPHORYLASE COMPLEXED WITH INOSINE AND SULFATE
ComponentsPURINE NUCLEOSIDE PHOSPHORYLASE
KeywordsPENTOSYLTRANSFERASE / PURINE NUCLEOSIDE PHOSPHORYLASE
Function / homologyPurine nucleoside phosphorylase / Nucleoside phosphorylase domain / Purine nucleoside phosphorylase I, inosine/guanosine-specific / Purine phosphorylase, family 2, conserved site / Nucleoside phosphorylase superfamily / Phosphorylase superfamily / Purine and other phosphorylases family 2 signature. / Neutrophil degranulation / Purine salvage / Purine catabolism ...Purine nucleoside phosphorylase / Nucleoside phosphorylase domain / Purine nucleoside phosphorylase I, inosine/guanosine-specific / Purine phosphorylase, family 2, conserved site / Nucleoside phosphorylase superfamily / Phosphorylase superfamily / Purine and other phosphorylases family 2 signature. / Neutrophil degranulation / Purine salvage / Purine catabolism / purine-nucleoside phosphorylase activity / purine-nucleoside phosphorylase / nucleoside metabolic process / cytoskeleton / cytoplasm / Purine nucleoside phosphorylase
Function and homology information
Specimen sourceBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 2 Å resolution
AuthorsMao, C. / Cook, W.J. / Zhou, M. / Fedorov, A.A. / Almo, S.C. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 1998
Title: Calf spleen purine nucleoside phosphorylase complexed with substrates and substrate analogues.
Authors: Mao, C. / Cook, W.J. / Zhou, M. / Federov, A.A. / Almo, S.C. / Ealick, S.E.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 10, 1998 / Release: Jul 15, 1998
RevisionDateData content typeGroupProviderType
1.0Jul 15, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PURINE NUCLEOSIDE PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4303
Polyers32,0651
Non-polymers3642
Water93752
1
A: PURINE NUCLEOSIDE PHOSPHORYLASE
hetero molecules

A: PURINE NUCLEOSIDE PHOSPHORYLASE
hetero molecules

A: PURINE NUCLEOSIDE PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,2899
Polyers96,1963
Non-polymers1,0936
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_656-z+1,x+1/2,-y+3/21
crystal symmetry operation11_466y-1/2,-z+3/2,-x+11
Buried area (Å2)9590
ΔGint (kcal/M)-107
Surface area (Å2)29180
MethodPISA,PQS
Unit cell
γ
α
β
Length a, b, c (Å)94.200, 94.200, 94.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP 21 3

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Components

#1: Protein/peptide PURINE NUCLEOSIDE PHOSPHORYLASE /


Mass: 32065.471 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / Genus: Bos / Organ: SPLEEN
References: UniProt: P55859, purine-nucleoside phosphorylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Formula: SO4 / Sulfate
#3: Chemical ChemComp-NOS / INOSINE


Mass: 268.226 Da / Num. of mol.: 1 / Formula: C10H12N4O5 / Inosine
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 / Density percent sol: 43.35 %
Crystal growDetails: PROTEIN WAS CRYSTALLIZED FROM 31-35% PEG-400 IN 100 MM HEPES BUFFER, PH 7.8-8.2; 100 MM MGCL2; 1% OCTYL-BETA- D-GLUCOPYRANOSIDE. CRYSTAL SOAKED IN 12.8 MM INOSINE AND 12 MM SULFATE.
PH range: 7.8-8.2
Crystal
*PLUS
Density percent sol: 65 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 8.2 / PH range high: 7.8
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDDetails
131-35 %PEG4001reservoir
2100 mMHEPES1reservoiror Tris-HCl
31 %beta-D-glucopyranoside1reservoir

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Data collection

DiffractionMean temperature: 296 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Collection date: Aug 1, 1996
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 2 Å / D resolution low: 8 Å / Number obs: 15060 / Percent possible obs: 83

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
SDMSdata reduction
SDMSdata scaling
X-PLOR3.8phasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PBN
R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 2
Displacement parametersB iso mean: 14 Å2
Least-squares processR factor R work: 0.18 / R factor obs: 0.18 / Highest resolution: 2 Å / Lowest resolution: 8 Å / Number reflection obs: 15060
Refine hist #LASTHighest resolution: 2 Å / Lowest resolution: 8 Å
Number of atoms included #LASTProtein: 2200 / Nucleic acid: 0 / Ligand: 24 / Solvent: 52 / Total: 2276
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.1
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.DNATOPH11.DNA
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1

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