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- PDB-3ut6: Crystal structure of E. Coli PNP complexed with PO4 and formycin A -

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Basic information

Entry
Database: PDB / ID: 3ut6
TitleCrystal structure of E. Coli PNP complexed with PO4 and formycin A
ComponentsPurine nucleoside phosphorylase deoD-type
KeywordsTRANSFERASE / purine nucleoside phosphorylase / formycin
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
Chem-FMC / PHOSPHATE ION / Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.895 Å
AuthorsStefanic, Z.
CitationJournal: Febs Lett. / Year: 2012
Title: New phosphate binding sites in the crystal structure of Escherichia coli purine nucleoside phosphorylase complexed with phosphate and formycin A.
Authors: Stefanic, Z. / Narczyk, M. / Mikleusevic, G. / Wielgus-Kutrowska, B. / Bzowska, A. / Luic, M.
History
DepositionNov 25, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 deoD-type
B: Purine nucleoside phosphorylase deoD-type
C: Purine nucleoside phosphorylase deoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,44111
Polymers77,1653
Non-polymers1,2778
Water11,223623
1
A: Purine nucleoside phosphorylase deoD-type
B: Purine nucleoside phosphorylase deoD-type
C: Purine nucleoside phosphorylase deoD-type
hetero molecules

A: Purine nucleoside phosphorylase deoD-type
B: Purine nucleoside phosphorylase deoD-type
C: Purine nucleoside phosphorylase deoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,88322
Polymers154,3306
Non-polymers2,55316
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area27210 Å2
ΔGint-199 kcal/mol
Surface area43700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.769, 120.769, 239.082
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-284-

HOH

21A-375-

HOH

31B-322-

HOH

41B-332-

HOH

51B-354-

HOH

61B-462-

HOH

71C-278-

HOH

81C-456-

HOH

91C-534-

HOH

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Components

#1: Protein Purine nucleoside phosphorylase deoD-type / PNP / Inosine phosphorylase


Mass: 25721.633 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12
References: UniProt: P0ABP8, purine-nucleoside phosphorylase
#2: Chemical ChemComp-FMC / (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol


Mass: 267.241 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 623 / 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: 3.26 Å3/Da / Density % sol: 62.28 %
Crystal growTemperature: 291 K / Method: hanging drop / pH: 5.2
Details: 50mM citrate buffer, 35% ammonium phosphate (w/v), pH 5.2, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 12, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.895→50 Å / Num. all: 80198 / Num. obs: 80026 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.8 % / Rmerge(I) obs: 0.146 / Χ2: 1.775 / Net I/σ(I): 5.4
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
1.9-1.939.439580.6191100
1.93-1.979.539540.65111000.906
1.97-2.018.839300.77711000.775
2.01-2.059.539400.82211000.669
2.05-2.099.539410.79611000.557
2.09-2.149.539680.83411000.485
2.14-2.199.539650.87611000.426
2.19-2.259.439690.94411000.365
2.25-2.329.439781.03911000.307
2.32-2.399.139711.10111000.277
2.39-2.489.339711.18211000.24
2.48-2.589.139861.26911000.214
2.58-2.78.940041.49199.90.176
2.7-2.84940191.694199.90.162
2.84-3.028.940132.095199.80.145
3.02-3.258.740503.211199.90.135
3.25-3.588.640334.932199.70.129
3.58-4.097.540535.378198.80.105
4.09-5.165.939994.821196.20.079
5.16-507.443243.519197.40.058

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.895→28.596 Å / Occupancy max: 1 / Occupancy min: 0.22 / FOM work R set: 0.8846 / SU ML: 0.17 / σ(F): 0 / Phase error: 17.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1871 1873 2.42 %RANDOM
Rwork0.1629 ---
all0.1642 82215 --
obs0.1635 77505 94.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.549 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso max: 101.93 Å2 / Biso mean: 31.2114 Å2 / Biso min: 14.69 Å2
Baniso -1Baniso -2Baniso -3
1-1.6206 Å2-0 Å2-0 Å2
2--1.6206 Å20 Å2
3----3.2412 Å2
Refinement stepCycle: LAST / Resolution: 1.895→28.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5384 0 82 623 6089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075691
X-RAY DIFFRACTIONf_angle_d1.1747710
X-RAY DIFFRACTIONf_chiral_restr0.072878
X-RAY DIFFRACTIONf_plane_restr0.004990
X-RAY DIFFRACTIONf_dihedral_angle_d13.5372118
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8948-1.9460.27111340.22465334546888
1.946-2.00320.2751320.20355351548389
2.0032-2.06790.21340.1835503563791
2.0679-2.14180.22061460.17185586573292
2.1418-2.22750.18371360.16325641577793
2.2275-2.32880.21191430.15665804594795
2.3288-2.45150.20351430.16285750589394
2.4515-2.6050.19911430.16365873601696
2.605-2.8060.19361460.175958610497
2.806-3.08810.17511510.17476025617697
3.0881-3.53420.19571490.16036126627598
3.5342-4.45010.14471530.13686168632198
4.4501-28.59910.18161630.16346513667698

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