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- PDB-3s5v: Structure of the cyanobacterial Oscillatoria Agardhii Agglutinin ... -

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Basic information

Entry
Database: PDB / ID: 3s5v
TitleStructure of the cyanobacterial Oscillatoria Agardhii Agglutinin (OAA) in free state obtained at -180 degrees 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: 1.55 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 ...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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1582
Polymers14,0621
Non-polymers961
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.899, 40.096, 68.986
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: PET26B / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2 DE3 / References: UniProt: C0STD7, UniProt: P84330*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 1.91 Å3/Da / Density % sol: 35.7 %
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: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 1, 2010
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.55→34.67 Å / Num. all: 16074 / Num. obs: 15223 / % possible obs: 98.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.024 / Net I/σ(I): 52.7
Reflection shellResolution: 1.55→1.59 Å / Rmerge(I) obs: 0.083 / Mean I/σ(I) obs: 7.1 / % possible all: 89.2

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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 3OBL

3obl


Resolution: 1.55→34.67 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.323 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19302 808 5 %RANDOM
Rwork0.18102 ---
obs0.18165 15223 98.68 %-
all-16074 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.693 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0 Å2-0 Å2
2---0.03 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.55→34.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms983 0 5 149 1137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211022
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.911399
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5995137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.04826.41553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.10815142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.149153
X-RAY DIFFRACTIONr_chiral_restr0.0980.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021831
X-RAY DIFFRACTIONr_mcbond_it0.7371.5649
X-RAY DIFFRACTIONr_mcangle_it1.23121029
X-RAY DIFFRACTIONr_scbond_it1.8413373
X-RAY DIFFRACTIONr_scangle_it2.664.5367
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 58 -
Rwork0.242 983 -
obs--88.37 %

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