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- PDB-3khs: Crystal structure of grouper iridovirus purine nucleoside phospho... -

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Basic information

Entry
Database: PDB / ID: 3khs
TitleCrystal structure of grouper iridovirus purine nucleoside phosphorylase
ComponentsPurine nucleoside phosphorylase
KeywordsHYDROLASE / alpha-beta structure / mixed beta-barrel
Function / homology
Function and homology information


nucleoside metabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity
Similarity search - Function
Purine nucleoside phosphorylase I, inosine/guanosine-specific / Purine nucleoside phosphorylase / 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
Similarity search - Component
Biological speciesGrouper iridovirus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsKang, Y.N. / Zhang, Y. / Allan, P.W. / Parker, W.B. / Ting, J.W. / Chang, C.Y. / Ealick, S.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Structure of grouper iridovirus purine nucleoside phosphorylase
Authors: Kang, Y.N. / Zhang, Y. / Allan, P.W. / Parker, W.B. / Ting, J.W. / Chang, C.Y. / Ealick, S.E.
History
DepositionOct 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase
B: Purine nucleoside phosphorylase
C: Purine nucleoside phosphorylase
D: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,33612
Polymers121,4684
Non-polymers8688
Water3,495194
1
A: Purine nucleoside phosphorylase
B: Purine nucleoside phosphorylase
C: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,7529
Polymers91,1013
Non-polymers6516
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-51 kcal/mol
Surface area30330 Å2
MethodPISA
2
D: Purine nucleoside phosphorylase
hetero molecules

D: Purine nucleoside phosphorylase
hetero molecules

D: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,7529
Polymers91,1013
Non-polymers6516
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area7770 Å2
ΔGint-47 kcal/mol
Surface area29000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.048, 193.048, 105.629
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Purine nucleoside phosphorylase


Mass: 30366.969 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Grouper iridovirus / Gene: GIV43 / Plasmid: pET-20b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): B834pLysS
References: UniProt: Q5YBA4, purine-nucleoside phosphorylase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.12 Å3/Da / Density % sol: 60.56 %
Crystal growTemperature: 275 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15-17% PEG 1000, 0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 275K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 21, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. all: 58889 / Num. obs: 56658 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 37.7 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 24.8
Reflection shellResolution: 2.38→2.47 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 3.1 / Num. unique all: 5946 / Rsym value: 0.404 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1ULA

1ula


Resolution: 2.38→44.65 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 340179.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 5745 10.1 %RANDOM
Rwork0.214 ---
all0.214 58889 --
obs0.214 56658 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.8847 Å2 / ksol: 0.336308 e/Å3
Displacement parametersBiso mean: 47.7 Å2
Baniso -1Baniso -2Baniso -3
1--6.51 Å21.82 Å20 Å2
2---6.51 Å20 Å2
3---13.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.38→44.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7894 0 52 194 8140
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.811.5
X-RAY DIFFRACTIONc_mcangle_it3.972
X-RAY DIFFRACTIONc_scbond_it4.522
X-RAY DIFFRACTIONc_scangle_it5.62.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.38→2.53 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.349 957 10.6 %
Rwork0.299 8056 -
obs--91.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4cis_peptide.paramtrs.top
X-RAY DIFFRACTION5trs.param

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