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- PDB-3ooe: Crystal structure of E. Coli purine nucleoside phosphorylase with PO4 -

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Basic information

Entry
Database: PDB / ID: 3ooe
TitleCrystal structure of E. Coli purine nucleoside phosphorylase with PO4
ComponentsPurine nucleoside phosphorylase deoD-type
KeywordsTRANSFERASE / purine nucleoside phosphorylase / phosphorylase
Function / homology
Function and homology information


purine nucleoside interconversion / guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / purine nucleoside catabolic process / 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
PHOSPHATE ION / : / Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMikleusevic, G. / Stefanic, Z. / Narzyk, M. / Wielgus-Kutrowska, B. / Bzowska, A. / Luic, M.
CitationJournal: Biochimie / Year: 2011
Title: Validation of the catalytic mechanism of Escherichia coli purine nucleoside phosphorylase by structural and kinetic studies.
Authors: Mikleusevic, G. / Stefanic, Z. / Narczyk, M. / Wielgus-Kutrowska, B. / Bzowska, A. / Luic, M.
History
DepositionAug 31, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
D: Purine nucleoside phosphorylase deoD-type
E: Purine nucleoside phosphorylase deoD-type
F: Purine nucleoside phosphorylase deoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,65920
Polymers154,3306
Non-polymers1,33014
Water20,0331112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21150 Å2
ΔGint-135 kcal/mol
Surface area44220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.076, 123.435, 189.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 25721.633 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: deoD, EcDH1_3614 / Plasmid: pSE380 / Production host: Escherichia coli (E. coli) / Strain (production host): HS533
References: UniProt: C9QST6, UniProt: P0ABP8*PLUS, purine-nucleoside phosphorylase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1112 / 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: 2.4 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 50mM citric buffer, 34% ammonium sulphate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95373 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: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2→47.463 Å / Num. all: 99205 / Num. obs: 97448 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 24.459 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 18.64
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obs% possible all
2-2.120.3860.4624.9121689158051523796.4
2.12-2.270.2590.3246.9117170149041456697.7
2.27-2.450.1830.239.4109128138861359397.9
2.45-2.680.1290.17212.3100973128461258097.9
2.68-30.0890.1217.191683116531146198.4
3-3.460.0470.06927.180815103481018898.5
3.46-4.230.0280.04539.9681088788869999
4.23-5.960.0230.03747.2526536918685299
5.96-47.60.0180.02752.7294084057401098.8

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XSCALEdata processing
PDB_EXTRACT3.006data extraction
HKL-2000data collection
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K9S

1k9s


Resolution: 2→47.46 Å / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.887 / SU ML: 0.14 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.196 4873 5 %RANDOM
Rwork0.15 ---
all0.155 99325 --
obs0.152 97186 98.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.609 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso max: 82.87 Å2 / Biso mean: 21.126 Å2 / Biso min: 6.97 Å2
Baniso -1Baniso -2Baniso -3
1--4.548 Å2-0 Å20 Å2
2---7.379 Å2-0 Å2
3---11.927 Å2
Refinement stepCycle: LAST / Resolution: 2→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10534 0 70 1112 11716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810811
X-RAY DIFFRACTIONf_angle_d1.05914578
X-RAY DIFFRACTIONf_chiral_restr0.0741654
X-RAY DIFFRACTIONf_plane_restr0.0041876
X-RAY DIFFRACTIONf_dihedral_angle_d15.0043903
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.0720.2184750.1729028950397
2.072-2.1540.2194800.179129960998
2.154-2.2530.2254800.1629104958498
2.253-2.3710.2114800.1539131961197
2.371-2.520.2154840.1529196968098
2.52-2.7140.1964840.1469190967498
2.714-2.9870.1994870.1519258974598
2.987-3.420.1734910.1379331982299
3.42-4.3080.1644970.1259438993599
4.308-47.4760.2055150.16397701028599

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