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- PDB-1a9t: BOVINE PURINE NUCLEOSIDE PHOSPHORYLASE COMPLEXED WITH 9-DEAZAINOS... -

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Basic information

Entry
Database: PDB / ID: 1a9t
TitleBOVINE PURINE NUCLEOSIDE PHOSPHORYLASE COMPLEXED WITH 9-DEAZAINOSINE AND PHOSPHATE
ComponentsPURINE NUCLEOSIDE PHOSPHORYLASE
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / PENTOSYLTRANSFERASE / 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: Jun 17, 1998
RevisionDateData content typeGroupProviderType
1.0Jun 17, 1998Structure modelrepositoryInitial release
1.1Mar 3, 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)31,9343
Polyers31,5681
Non-polymers3662
Water1,00956
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)95,8039
Polyers94,7043
Non-polymers1,0996
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)9570
ΔGint (kcal/M)-44
Surface area (Å2)29260
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: 31567.992 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / Genus: Bos / Organ: SPLEEN
References: UniProt: P55859, purine-nucleoside phosphorylase
#2: Chemical ChemComp-R1P / RIBOSE-1-PHOSPHATE


Mass: 230.110 Da / Num. of mol.: 1 / Formula: C5H11O8P / Ribose 5-phosphate
#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.: 56 / 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: 2.21 / Density percent sol: 44.23 %
Crystal growDetails: PROTEIN WAS CRYSTALLIZED FROM 31-35% PEG-400 IN 100 MM HEPES OR TRIS BUFFER, PH 7.8-8.2; 100 MM MGCL2; 1% OCTYL-BETA- D-GLUCOPYRANOSIDE
PH range: 7.8-8.2
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 8.2 / PH range high: 7.8
components of the solutions
*PLUS

Crystal ID: 1

IDConcCommon nameSol IDDetailsChemical formula
130-40 mg/mlproteindrop
210 mMHEPESdrop
331-35 %PEG400reservoir
4100 mMHEPESreservoiror Tris-HCl buffer
5100 mMreservoirMgCl2
61 %octyl beta-D-glucopyranosidereservoir

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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: 14891 / Percent possible obs: 8

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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: 15 Å2
Least-squares processR factor R work: 0.19 / R factor obs: 0.19 / Highest resolution: 2 Å / Lowest resolution: 8 Å / Number reflection obs: 14891
Refine hist #LASTHighest resolution: 2 Å / Lowest resolution: 8 Å
Number of atoms included #LASTProtein: 2215 / Nucleic acid: 0 / Ligand: 24 / Solvent: 56 / Total: 2295
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_deg1.6
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_d1.2
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_deg1.2

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