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- PDB-1a69: PURINE NUCLEOSIDE PHOSPHORYLASE IN COMPLEX WITH FORMYCIN B AND SU... -

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Basic information

Entry
Database: PDB / ID: 1a69
TitlePURINE NUCLEOSIDE PHOSPHORYLASE IN COMPLEX WITH FORMYCIN B AND SULPHATE (PHOSPHATE)
ComponentsPURINE NUCLEOSIDE PHOSPHORYLASE
KeywordsGLYCOSYLTRANSFERASE / PURINE NUCLEOSIDE PHOSPHORYLASE / TRANSFERASE
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
FORMYCIN B / Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKoellner, G. / Luic, M. / Shugar, D. / Saenger, W. / Bzowska, A.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Crystal structure of the ternary complex of E. coli purine nucleoside phosphorylase with formycin B, a structural analogue of the substrate inosine, and phosphate (Sulphate) at 2.1 A resolution.
Authors: Koellner, G. / Luic, M. / Shugar, D. / Saenger, W. / Bzowska, A.
History
DepositionMar 8, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6459
Polymers77,5523
Non-polymers1,0936
Water6,774376
1
A: PURINE NUCLEOSIDE PHOSPHORYLASE
B: PURINE NUCLEOSIDE PHOSPHORYLASE
C: PURINE NUCLEOSIDE PHOSPHORYLASE
hetero molecules

A: PURINE NUCLEOSIDE PHOSPHORYLASE
B: PURINE NUCLEOSIDE PHOSPHORYLASE
C: PURINE NUCLEOSIDE PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,29018
Polymers155,1046
Non-polymers2,18612
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area26110 Å2
ΔGint-256 kcal/mol
Surface area42930 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)123.110, 123.110, 241.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-241-

HOH

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Components

#1: Protein PURINE NUCLEOSIDE PHOSPHORYLASE /


Mass: 25850.748 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
References: UniProt: P0ABP8, purine-nucleoside phosphorylase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FMB / FORMYCIN B


Mass: 268.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H12N4O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 3.67 Å3/Da / Density % sol: 70 %
Crystal growpH: 5.3
Details: 28-35% AMMONIUM SULPHATE, 50 MM CITRATE BUFFER, PH 5.2-5.4, pH 5.3
PH range: 5.2-5.4
Crystal
*PLUS
Crystal grow
*PLUS
pH: 5.4 / Method: vapor diffusion, hanging drop / Details: Cook, W.J., (1985) J. Biol. Chem., 260, 12968.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
215 %satammonium sulfate1drop
30.025 Mcitrate1drop
430 %satammonium sulfate1reservoir
50.05 Mcitrate1reservoir

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Data collection

DiffractionMean temperature: 281 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 668538 / % possible obs: 98.3 % / Observed criterion σ(I): 1 / Redundancy: 9.2 % / Biso Wilson estimate: 22.8 Å2 / Rsym value: 0.137 / Net I/σ(I): 7.9
Reflection shellResolution: 2.1→2.2 Å / Rsym value: 0.297 / % possible all: 98
Reflection
*PLUS
Num. obs: 72585 / Num. measured all: 668538 / Rmerge(I) obs: 0.137
Reflection shell
*PLUS
Rmerge(I) obs: 0.297

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ECP

1ecp


Resolution: 2.1→20 Å / Isotropic thermal model: 1 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO /
RfactorNum. reflection% reflection
obs0.196 72585 98.3 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 207 Å2 / ksol: 0.8 e/Å3
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5298 0 72 376 5746
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.005108471
X-RAY DIFFRACTIONt_angle_deg1.301146092
X-RAY DIFFRACTIONt_dihedral_angle_d24.56572
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.0021617100
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg24.5
X-RAY DIFFRACTIONt_plane_restr0.002100

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