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- PDB-1k9s: PURINE NUCLEOSIDE PHOSPHORYLASE FROM E. COLI IN COMPLEX WITH FORM... -

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Basic information

Entry
Database: PDB / ID: 1k9s
TitlePURINE NUCLEOSIDE PHOSPHORYLASE FROM E. COLI IN COMPLEX WITH FORMYCIN A DERIVATIVE AND PHOSPHATE
ComponentsPURINE NUCLEOSIDE PHOSPHORYLASE
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / PURINE NUCLEOSIDE PHOSPHORYLASE / E. COLI
Function / homology
Function and homology information


purine nucleoside interconversion / guanosine phosphorylase activity / purine nucleoside catabolic process / purine-nucleoside phosphorylase activity / purine-nucleoside phosphorylase / DNA damage response / identical protein binding / membrane / 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
Chem-FM1 / Chem-FM2 / PHOSPHATE ION / Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKoellner, G. / Bzowska, A. / Wielgus-Kutrowska, B. / Luic, M. / Steiner, T. / Saenger, W. / Stepinski, J.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Open and closed conformation of the E. coli purine nucleoside phosphorylase active center and implications for the catalytic mechanism.
Authors: Koellner, G. / Bzowska, A. / Wielgus-Kutrowska, B. / Luic, M. / Steiner, T. / Saenger, W. / Stepinski, J.
History
DepositionOct 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,59018
Polymers154,3306
Non-polymers2,26012
Water22,3031238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26880 Å2
ΔGint-178 kcal/mol
Surface area43010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.779, 178.779, 167.943
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
PURINE NUCLEOSIDE PHOSPHORYLASE


Mass: 25721.633 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
References: UniProt: P0ABP8, purine-nucleoside phosphorylase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-FM2 / 2-(7-AMINO-6-METHYL-3H-PYRAZOLO[4,3-D]PYRIMIDIN-3-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL / 6-METHYL-FORMYCIN A


Mass: 282.276 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H16N5O4
#4: Chemical ChemComp-FM1 / 2-HYDROXYMETHYL-5-(7-METHYLAMINO-3H-PYRAZOLO[4,3-D]PYRIMIDIN-3-YL)-TETRAHYDRO-FURAN-3,4-DIOL / N7-METHYL-FORMYCIN A


Mass: 281.268 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H15N5O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1238 / 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: 4.35 Å3/Da / Density % sol: 71.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 28-35% ammonium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 5.4 / 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: 290 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9095 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 23, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9095 Å / Relative weight: 1
ReflectionResolution: 2→19.95 Å / Num. obs: 178749 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.106
Reflection shellResolution: 2→2.13 Å / % possible all: 97.6
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 622701
Reflection shell
*PLUS
Lowest resolution: 2.2 Å / % possible obs: 97.3 % / Rmerge(I) obs: 0.412

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.95 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 5548199.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.184 17760 9.9 %RANDOM
Rwork0.161 ---
obs0.161 178749 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.3701 Å2 / ksol: 0.337517 e/Å3
Displacement parametersBiso mean: 24.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2--0.39 Å20 Å2
3----0.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10890 0 149 1238 12277
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.831.5
X-RAY DIFFRACTIONc_mcangle_it1.392
X-RAY DIFFRACTIONc_scbond_it3.622
X-RAY DIFFRACTIONc_scangle_it4.232.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.004 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.231 2917 10 %
Rwork0.22 26396 -
obs--97.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PO4.PARAMPO4.TOP
X-RAY DIFFRACTION3FMA.PARAMFMA.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.3 % / Rfactor Rfree: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.97
X-RAY DIFFRACTIONc_mcbond_it0.831.5
X-RAY DIFFRACTIONc_scbond_it3.622
X-RAY DIFFRACTIONc_mcangle_it1.392
X-RAY DIFFRACTIONc_scangle_it4.232.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.231 / % reflection Rfree: 10 % / Rfactor Rwork: 0.22

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