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- PDB-1a9q: BOVINE PURINE NUCLEOSIDE PHOSPHORYLASE COMPLEXED WITH INOSINE -

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Basic information

Entry
Database: PDB / ID: 1a9q
TitleBOVINE PURINE NUCLEOSIDE PHOSPHORYLASE COMPLEXED WITH INOSINE
ComponentsPURINE NUCLEOSIDE PHOSPHORYLASE
KeywordsPENTOSYLTRANSFERASE / PURINE NUCLEOSIDE PHOSPHORYLASE
Function/homologyPurine catabolism / Purine salvage / Purine nucleoside phosphorylase I, inosine/guanosine-specific / Purine nucleoside phosphorylase / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / purine-nucleoside phosphorylase activity / purine-nucleoside phosphorylase / Neutrophil degranulation / nucleoside metabolic process ...Purine catabolism / Purine salvage / Purine nucleoside phosphorylase I, inosine/guanosine-specific / Purine nucleoside phosphorylase / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / purine-nucleoside phosphorylase activity / purine-nucleoside phosphorylase / Neutrophil degranulation / nucleoside metabolic process / Nucleoside phosphorylase domain / Nucleoside phosphorylase superfamily / Phosphorylase superfamily / cytoskeleton / cytoplasm / Purine nucleoside phosphorylase
Function and homology information
Specimen sourceBos taurus / mammal / Cattle /
MethodX-ray diffraction (2 Å resolution / Molecular replacement) / X-ray crystallography
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

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Assembly

Deposited unit
A: PURINE NUCLEOSIDE PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6613
Polyers31,4291
Non-polymers2322
Water99155
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)94,9839
Polyers94,2863
Non-polymers6976
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)8590
ΔGint (kcal/M)-74
Surface area (Å2)29870
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: 31428.799 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / mammal / Cattle / / Genus: Bos / Organ: SPLEEN
References: UniProt:P55859, EC:2.4.2.1 (purine-nucleoside phosphorylase)
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 136.111 Da / Num. of mol.: 1 / Formula: C5H4N4O / : Hypoxanthine
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Formula: H2O / : Water
Nonpolymer detailsTHE INOSINE SOAK RESULTS IN AN APPARENT HYDROLYSIS BY PURINE NUCLEOSIDE PHOSPHORYLASE. ONLY ...THE INOSINE SOAK RESULTS IN AN APPARENT HYDROLYSIS BY PURINE NUCLEOSIDE PHOSPHORYLASE. ONLY HYPOXANTHINE IS SEEN IN THE ACTIVE SITE. SULFATE CONTAMINANT AY COME FROM THE HEPES BUFFER, AND IT CUASES APPROXIMATELY 50% OCCUPANCY OF SULFATE IN THE PHOSPHATE BINDING SITE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.22 / Density percent sol: 44.48
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 ARTI- FICIAL MOTHER LIQUOR CONTAINING 7.3 MM INOSINE.
PH range: 7.8-8.2
Crystal
*PLUS
Density percent sol: 65
Crystal grow
*PLUS
Temp unit: unknown / Method: Vapor diffusion, hanging drop / PH range low: 8.2 / PH range high: 7.8
Crystal grow comp
*PLUS

Crystal ID: 1 / Sol ID: reservoir

IDConcConc unitCommon nameDetails
131-35%PEG400
2100mMHEPESor Tris-HCl
31%beta-D-glucopyranoside

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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: 15990 / Percent possible obs: 89

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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: 19 Å2
Least-squares processR factor R work: 0.2 / R factor obs: 0.2 / Highest resolution: 2 Å / Lowest resolution: 8 Å / Number reflection obs: 15990
Refine hist #LASTHighest resolution: 2 Å / Lowest resolution: 8 Å
Number of atoms included #LASTProtein: 2194 / Nucleic acid: 0 / Ligand: 15 / Solvent: 55 / Total: 2264
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
Least-squares process
*PLUS
R factor R work: 0.2 / R factor obs: 0.2
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1

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