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- PDB-1ecp: PURINE NUCLEOSIDE PHOSPHORYLASE -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1ecp
TitlePURINE NUCLEOSIDE PHOSPHORYLASE
ComponentsPURINE NUCLEOSIDE PHOSPHORYLASE
KeywordsPENTOSYLTRANSFERASE / PURINE NUCLEOSIDE PHOSPHORYLASE / GLYCOSYLTRANSFERASE
Function / homology
Function and homology information


purine nucleoside interconversion / guanosine phosphorylase activity / purine nucleoside catabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / DNA damage response / membrane / identical protein binding / cytosol
Similarity search - Function
Purine nucleoside phosphorylase DeoD-type / Nucleoside phosphorylase, conserved site / Purine and other phosphorylases family 1 signature. / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsMao, C. / Ealick, S.E.
CitationJournal: Structure / Year: 1997
Title: The crystal structure of Escherichia coli purine nucleoside phosphorylase: a comparison with the human enzyme reveals a conserved topology.
Authors: Mao, C. / Cook, W.J. / Zhou, M. / Koszalka, G.W. / Krenitsky, T.A. / Ealick, S.E.
History
DepositionJul 13, 1995Processing site: BNL
Revision 1.0Jun 20, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PURINE NUCLEOSIDE PHOSPHORYLASE
B: PURINE NUCLEOSIDE PHOSPHORYLASE
C: PURINE NUCLEOSIDE PHOSPHORYLASE
D: PURINE NUCLEOSIDE PHOSPHORYLASE
E: PURINE NUCLEOSIDE PHOSPHORYLASE
F: PURINE NUCLEOSIDE PHOSPHORYLASE


Theoretical massNumber of molelcules
Total (without water)155,1046
Polymers155,1046
Non-polymers00
Water8,647480
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20680 Å2
ΔGint-127 kcal/mol
Surface area46050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.500, 110.600, 74.600
Angle α, β, γ (deg.)90.00, 111.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PURINE NUCLEOSIDE PHOSPHORYLASE /


Mass: 25850.748 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: PBR322-DEO / Gene (production host): DEO OPERON / Production host: Escherichia coli (E. coli) / Strain (production host): BAU-1
References: UniProt: P0ABP8, purine-nucleoside phosphorylase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 480 / Source method: isolated from a natural source / Formula: H2O
Source detailsMOLECULE_NAME: PURINE NUCLEOSIDE PHOSPHORYLASE. THE PROTEIN WAS PURCHASED FROM SIGMA CO. THE ...MOLECULE_NAME: PURINE NUCLEOSIDE PHOSPHORYLASE. THE PROTEIN WAS PURCHASED FROM SIGMA CO. THE DETAILS OF THE PROTEIN PREPARATION ARE UNKNOWN.

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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 Å3/Da / Density % sol: 44.38 %
Crystal
*PLUS
Density % sol: 45 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 5 / PH range high: 4.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112-14 %PEG40001reservoir
250 mMcitrate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE MARK II / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 71593 / % possible obs: 70 % / Observed criterion σ(I): 1 / Redundancy: 3.26 % / Rmerge(I) obs: 0.0875
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 70600 / Num. measured all: 230200 / Rmerge(I) obs: 0.087

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 2→15 Å / σ(F): 2 /
RfactorNum. reflection
Rfree0.29 -
Rwork0.2 -
obs0.2 70600
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10758 0 0 480 11238
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_d
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
Refinement
*PLUS
Lowest resolution: 8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_deg23.8
X-RAY DIFFRACTIONx_improper_angle_deg1.1

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