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- PDB-3s60: Structure of the cyanobacterial Oscillatoria Agardhii Agglutinin ... -

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Basic information

Entry
Database: PDB / ID: 3s60
TitleStructure of the cyanobacterial Oscillatoria Agardhii Agglutinin (OAA) in free state obtained at 25 degree Celsius
ComponentsLectin
KeywordsPROTEIN BINDING / BETA BARREL LIKE FOLD / ANTI-HIV LECTIN / CARBOHYDRATE
Function / homology
Function and homology information


D-mannose binding / carbohydrate binding
Similarity search - Function
Lipocalin - #450 / OAA-family lectin sugar binding domain / : / OAA-family lectin sugar binding domain / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesPlanktothrix agardhii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKoharudin, L.M.I. / Gronenborn, A.M.
Citation
Journal: Structure / Year: 2011
Title: Structural basis of the anti-HIV activity of the cyanobacterial Oscillatoria Agardhii agglutinin.
Authors: Koharudin, L.M. / Gronenborn, A.M.
#1: Journal: J.Biol.Chem. / Year: 2011
Title: Novel fold and carbohydrate specificity of the potent anti-HIV cyanobacterial lectin from Oscillatoria agardhii.
Authors: Koharudin, L.M. / Furey, W. / Gronenborn, A.M.
History
DepositionMay 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 25, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lectin


Theoretical massNumber of molelcules
Total (without water)14,0621
Polymers14,0621
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.467, 40.658, 70.374
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lectin


Mass: 14061.952 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planktothrix agardhii (bacteria) / Gene: OAA / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2 DE3 / References: UniProt: C0STD7, UniProt: P84330*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.01 Å3/Da / Density % sol: 38.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2.0 M (NH4)SO4 and 0.1 M Tris-HCl (pH 8.5), VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 1, 2010
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→26.61 Å / Num. all: 13272 / Num. obs: 13272 / % possible obs: 95 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2 / Redundancy: 2.48 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 8.7
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 1.5 / % possible all: 91.5

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0044refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3S5V

3s5v


Resolution: 1.6→26.61 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.972 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22793 1490 10.1 %RANDOM
Rwork0.18242 ---
obs0.18706 13272 94.98 %-
all-13272 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.666 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0 Å20 Å2
2---0.38 Å2-0 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.6→26.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms983 0 0 62 1045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0211031
X-RAY DIFFRACTIONr_angle_refined_deg1.9331.9051415
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3565141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.55926.48154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.05415145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.582153
X-RAY DIFFRACTIONr_chiral_restr0.1620.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021843
X-RAY DIFFRACTIONr_mcbond_it4.451.5655
X-RAY DIFFRACTIONr_mcangle_it5.63421043
X-RAY DIFFRACTIONr_scbond_it6.6243376
X-RAY DIFFRACTIONr_scangle_it8.064.5367
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 99 -
Rwork0.247 957 -
obs--91.27 %

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