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- PDB-3opv: Crystal structure of E. Coli purine nucleoside phosphorylase Arg2... -

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Basic information

Entry
Database: PDB / ID: 3opv
TitleCrystal structure of E. Coli purine nucleoside phosphorylase Arg24Ala mutant
ComponentsPurine nucleoside phosphorylase deoD-type
KeywordsTRANSFERASE / purine nucleoside phosphorylase / phosphorylase
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
PHOSPHATE ION / : / Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 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
DepositionSep 2, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
G: Purine nucleoside phosphorylase deoD-type
H: Purine nucleoside phosphorylase deoD-type
I: Purine nucleoside phosphorylase deoD-type
J: Purine nucleoside phosphorylase deoD-type
K: Purine nucleoside phosphorylase deoD-type
L: Purine nucleoside phosphorylase deoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)308,95626
Polymers307,62612
Non-polymers1,33014
Water26,8961493
1
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)154,38312
Polymers153,8136
Non-polymers5706
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20680 Å2
ΔGint-136 kcal/mol
Surface area46390 Å2
MethodPISA
2
G: Purine nucleoside phosphorylase deoD-type
H: Purine nucleoside phosphorylase deoD-type
I: Purine nucleoside phosphorylase deoD-type
J: Purine nucleoside phosphorylase deoD-type
K: Purine nucleoside phosphorylase deoD-type
L: Purine nucleoside phosphorylase deoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,57314
Polymers153,8136
Non-polymers7608
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20630 Å2
ΔGint-136 kcal/mol
Surface area46410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.207, 158.785, 122.240
Angle α, β, γ (deg.)90.000, 93.800, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11G-1249-

HOH

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Components

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


Mass: 25635.518 Da / Num. of mol.: 12 / Mutation: R24A
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.: 1493 / 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: 48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 30% ammonium sulphate, 50mM citric buffer , pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54128 Å
DetectorType: OXFORD RUBY CCD / Detector: CCD / Details: MICROFOCUS X-RAY TUBE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54128 Å / Relative weight: 1
ReflectionRedundancy: 4.7 % / Rmerge(I) obs: 0.084 / D res high: 2.4 Å / D res low: 19.12 Å
ReflectionResolution: 2.4→19.116 Å / Num. all: 111867 / Num. obs: 111867 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Rmerge(I) allMean I/σ(I) allNum. measured allNum. unique allDiffraction-ID% possible all
2.4-2.530.362.149258163201100
2.53-2.680.262.8649769154461100
2.68-2.870.213.4355249145361100
2.87-3.10.164.5860259135461100
3.1-3.390.116.2459154124501100
3.39-3.790.097.3558784113151100
3.79-4.380.0610.036382699581100
4.38-5.370.0512.126004184081100
5.37-7.590.0512.134644365541100
7.59-19.120.0412.87227153383193.38

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 42.02
Highest resolutionLowest resolution
Rotation2.5 Å19.12 Å
Translation2.5 Å19.12 Å

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.9 2008/10/21data scaling
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K9S

1k9s


Resolution: 2.4→19.1 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.826 / SU ML: 0.51 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1767 1.58 %RANDOM
Rwork0.181 ---
all0.182 111922 --
obs0.182 110205 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.476 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso max: 117.68 Å2 / Biso mean: 34.081 Å2 / Biso min: 10.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.583 Å2-0 Å2-1.069 Å2
2---6.82 Å2-0 Å2
3---6.237 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21389 0 70 1493 22952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00421825
X-RAY DIFFRACTIONf_angle_d0.77829445
X-RAY DIFFRACTIONf_chiral_restr0.0533363
X-RAY DIFFRACTIONf_plane_restr0.0033807
X-RAY DIFFRACTIONf_dihedral_angle_d13.8077839
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4-2.4860.3391720.2481096411136
2.486-2.5850.2831770.2221099311170
2.585-2.7020.2611850.2031095311138
2.702-2.8440.2821700.2231101511185
2.844-3.0220.3291850.2261096211147
3.022-3.2540.2871780.2031097811156
3.254-3.580.2191700.1741105911229
3.58-4.0930.221790.1481104011219
4.093-5.140.1591740.1311102211196
5.14-19.1160.1881770.161111411291

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