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- PDB-4ldn: Crystal structure of a putative purine nucleoside phosphorylase f... -

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Basic information

Entry
Database: PDB / ID: 4ldn
TitleCrystal structure of a putative purine nucleoside phosphorylase from Vibrio fischeri ES114 (Target NYSGRC-029521)
ComponentsPurine nucleoside phosphorylase DeoD-type
KeywordsTRANSFERASE / Structural genomics / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


purine nucleoside metabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity
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 speciesVibrio fischeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.48 Å
AuthorsSampathkumar, P. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: to be published
Title: Crystal structure of a putative purine nucleoside phosphorylase from Vibrio fischeri ES114 (Target NYSGRC-029521)
Authors: Sampathkumar, P. / Ahmed, M. / Attonito, J. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Eromenok, G. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Himmel, D.M. / Hillerich, B. / ...Authors: Sampathkumar, P. / Ahmed, M. / Attonito, J. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Eromenok, G. / Fiser, A. / Glenn, A.S. / Hammonds, J. / Himmel, D.M. / Hillerich, B. / Khafizov, K. / Lafleur, J. / Love, J.D. / Stead, M. / Seidel, R. / Toro, R. / Morisco, L.L. / Sojitra, S.S. / Wasserman, S.R. / Suarez, J. / Schramm, V.L. / Almo, S.C.
History
DepositionJun 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2428
Polymers29,7421
Non-polymers5007
Water2,954164
1
A: Purine nucleoside phosphorylase DeoD-type
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)181,45248
Polymers178,4506
Non-polymers3,00242
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area28020 Å2
ΔGint-82 kcal/mol
Surface area51840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.115, 163.115, 45.339
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-306-

EDO

21A-432-

HOH

31A-457-

HOH

41A-477-

HOH

51A-533-

HOH

Detailsprobable hexamer

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Components

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


Mass: 29741.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio fischeri (bacteria) / Strain: ES114 / Gene: deoD3, VF_A0968 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus RIL
References: UniProt: Q5DYV8, purine-nucleoside phosphorylase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 1.95 Å3/Da / Density % sol: 36.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: Protein (20mM HEPES pH7.5, 150mM NaCl, 5% glycerol, and 5mM DTT), Reservoir (MCSG2 #05 - 0.2 M Lithium Sulfate, 0.1 M CAPS:NaOH pH 10.5, 1.2 M NaH2PO4/0.8 M K2HPO4), Cryoprotection (33% ...Details: Protein (20mM HEPES pH7.5, 150mM NaCl, 5% glycerol, and 5mM DTT), Reservoir (MCSG2 #05 - 0.2 M Lithium Sulfate, 0.1 M CAPS:NaOH pH 10.5, 1.2 M NaH2PO4/0.8 M K2HPO4), Cryoprotection (33% Ethylene glycol), VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 18, 2013 / Details: MIRRORS
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.48→40 Å / Num. obs: 37977 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 14.8 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 23.7
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.801 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1837 / % possible all: 96.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
XDSdata reduction
Aimlessdata scaling
SHELXCphasing
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.48→30.84 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.41 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.187 1896 5 %RANDOM
Rwork0.1624 ---
obs0.1636 37970 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 66.62 Å2 / Biso mean: 18.3874 Å2 / Biso min: 7.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å2-0.62 Å2-0 Å2
2---0.62 Å2-0 Å2
3---2.01 Å2
Refinement stepCycle: LAST / Resolution: 1.48→30.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1901 0 30 164 2095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192037
X-RAY DIFFRACTIONr_bond_other_d0.0020.021969
X-RAY DIFFRACTIONr_angle_refined_deg1.6361.9852765
X-RAY DIFFRACTIONr_angle_other_deg0.76834535
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0045266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11824.36294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39715322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0661512
X-RAY DIFFRACTIONr_chiral_restr0.0870.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022310
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02464
X-RAY DIFFRACTIONr_mcbond_it1.2511.574999
X-RAY DIFFRACTIONr_mcbond_other1.2481.57998
X-RAY DIFFRACTIONr_mcangle_it2.1192.3541253
LS refinement shellResolution: 1.483→1.521 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 144 -
Rwork0.256 2607 -
all-2751 -
obs-2607 97.8 %

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