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- PDB-2b94: Structural analysis of P knowlesi homolog of P falciparum PNP -

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Basic information

Entry
Database: PDB / ID: 2b94
TitleStructural analysis of P knowlesi homolog of P falciparum PNP
Componentspurine nucleoside phosphorylase
KeywordsTRANSFERASE / SGPP / Structural Genomics / PSI / Protein Structure Initiative / PNP / UDP / Ontario/Toronto SGC / Structural Genomics of Pathogenic Protozoa Consortium
Function / homologyNucleoside phosphorylase domain / Phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / THIOSULFATE
Function and homology information
Biological speciesPlasmodium knowlesi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsRobien, M.A. / Bosch, J. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: To be Published
Title: Structural analysis of P knowlesi homolog of P falciparum PNP
Authors: Robien, M.A. / Bosch, J. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
History
DepositionOct 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 23, 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
Remark 999SEQUENCE The sequence of this protein is not available at either SWS or GB sequence database at the ...SEQUENCE The sequence of this protein is not available at either SWS or GB sequence database at the time of processing. This protein is a homolog of Plasmodium falciparum PFE0660c, gi:23613155. The sequence is present in TargetDB as Pkno008421AAA. The sequence cited is based on P knowlesi genomic nucleotide sequence (plasmoDBv4.4: ORF id as of 10/12/2005: Pk_6f05p1c). The N-terminus residues -25-0 are cloning artifacts.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1343
Polymers29,9091
Non-polymers2242
Water2,396133
1
A: purine nucleoside phosphorylase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)180,80218
Polymers179,4576
Non-polymers1,34612
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 operation10_445y-1/3,x-2/3,-z+1/31
crystal symmetry operation11_455x-y-1/3,-y+1/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Unit cell
Length a, b, c (Å)98.377, 98.377, 160.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-306-

HOH

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Components

#1: Protein purine nucleoside phosphorylase


Mass: 29909.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium knowlesi (eukaryote) / Plasmid: PET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21STAR(DE3) / References: purine-nucleoside phosphorylase
#2: Chemical ChemComp-THJ / THIOSULFATE


Mass: 112.128 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O3S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.5 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: sodium thiosulfate, MOPS, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9184 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 27, 2004
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.85→41.1693 Å / Num. all: 24916 / Num. obs: 24916 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 24.193 Å2 / Rsym value: 0.87 / Net I/σ(I): 13
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.781 / % possible all: 81.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 1SQ6, 1NW4

1sq6

1nw4


Resolution: 1.85→14.99 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.806 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. A patch of density which could not be confidently assigned to components of the crystallization drop or known substrates remains in the ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. A patch of density which could not be confidently assigned to components of the crystallization drop or known substrates remains in the final difference maps. This density is bound roughly by residues 19, 20, 85, 86, 87, 88, 158 and 180.
RfactorNum. reflection% reflectionSelection details
Rfree0.22498 1257 5.1 %RANDOM
Rwork0.18674 ---
all0.18859 23591 --
obs0.18859 23591 96.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.461 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.85→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1807 0 10 133 1950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221845
X-RAY DIFFRACTIONr_bond_other_d0.0010.021710
X-RAY DIFFRACTIONr_angle_refined_deg1.1521.9772504
X-RAY DIFFRACTIONr_angle_other_deg0.75133955
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3595239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.63224.47867
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.33415309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.175158
X-RAY DIFFRACTIONr_chiral_restr0.0630.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022029
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02342
X-RAY DIFFRACTIONr_nbd_refined0.1950.2354
X-RAY DIFFRACTIONr_nbd_other0.1710.21682
X-RAY DIFFRACTIONr_nbtor_refined0.1670.2925
X-RAY DIFFRACTIONr_nbtor_other0.080.21026
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2120
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.29
X-RAY DIFFRACTIONr_mcbond_it2.04541277
X-RAY DIFFRACTIONr_mcbond_other0.4734492
X-RAY DIFFRACTIONr_mcangle_it2.82661935
X-RAY DIFFRACTIONr_scbond_it3.216696
X-RAY DIFFRACTIONr_scangle_it4.1378569
LS refinement shellResolution: 1.85→1.948 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.284 141 -
Rwork0.253 2832 -
obs--80.99 %

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