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- PDB-3obl: Crystal structure of the potent anti-HIV cyanobacterial lectin fr... -

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Basic information

Entry
Database: PDB / ID: 3obl
TitleCrystal structure of the potent anti-HIV cyanobacterial lectin from Oscillatoria Agardhii
ComponentsLectin
KeywordsSUGAR BINDING PROTEIN / novel beta barrel fold / anti-HIV lectin / High mannose glycans
Function / homologyLipocalin - #450 / OAA-family lectin sugar binding domain / OAA-family lectin sugar binding domain / Lipocalin / carbohydrate binding / Beta Barrel / Mainly Beta / Lectin
Function and homology information
Biological speciesPlanktothrix agardhii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.2 Å
AuthorsKoharudin, L.M.I. / Furey, W. / Gronenborn, A.M.
Citation
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.
#1: Journal: J.Biol.Chem. / Year: 2007
Title: Primary structure and carbohydrate binding specificity of a potent anti-HIV lectin isolated from the filamentous cyanobacterium Oscillatoria agardhii
Authors: Sato, Y. / Okuyama, S. / Hori, K.
#2: Journal: Fisheries Sci. / Year: 2009
Title: Cloning, expression, and characterization of a novel anti-HIV lectin from the cultured cyanobacterium, Oscillatoria agardhii
Authors: Sato, T. / Hori, K.
History
DepositionAug 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7476
Polymers27,8622
Non-polymers8854
Water6,197344
1
A: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3733
Polymers13,9311
Non-polymers4432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3733
Polymers13,9311
Non-polymers4432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.752, 47.275, 47.367
Angle α, β, γ (deg.)78.16, 62.99, 63.14
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Lectin /


Mass: 13930.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Expressed as native protein / Source: (gene. exp.) Planktothrix agardhii (bacteria) / Gene: OAA / Plasmid: pET26B(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: C0STD7
#2: Chemical
ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID / CAPS (buffer)


Mass: 221.317 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.71 Å3/Da / Density % sol: 54.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.2 M NaH2PO4/0.8 M K2HPO4, 0.2 M Li2SO4, 0.1 M CAPS (pH 10.5), VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9795, 0.9793, 0.9718
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 25, 2010 / Details: MIRRORS
RadiationMonochromator: ROSENBAUM-ROCK MONOCHROMATOR HIGH-RESOLUTION DOUBLE-CRYSTAL SI(220) SAGITTAL FOCUSING, ROSENBAUM- ROCK VERTICAL FOCUSING MIRROR
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97931
30.97181
ReflectionResolution: 1.1→22.64 Å / Num. obs: 86175 / % possible obs: 92 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 3.81 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 7.5
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 3.73 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 2.1 / Num. unique all: 9892 / % possible all: 83.1

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Processing

Software
NameVersionClassification
d*TREKdata scaling
PHENIXmodel building
PHASERphasing
REFMAC5.5.0044refinement
d*TREKdata reduction
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.2→22.64 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.692 / SU ML: 0.033 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE DATA HAVE BEEN COLLECTED UP 1.10 A RESOLUTION. HOWEVER, REFINEMENT CONVERGED TO BETTER R VALUES BY CUTTING THE RESOLUTION TO 1.20 A.
RfactorNum. reflection% reflectionSelection details
Rfree0.16923 8658 10 %RANDOM
Rwork0.14024 ---
all-77522 --
obs-77522 93.46 %-
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: 13.854 Å2
Baniso -1Baniso -2Baniso -3
1-2.76 Å20.19 Å2-1.34 Å2
2---1.23 Å20.5 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.2→22.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 56 344 2366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212262
X-RAY DIFFRACTIONr_bond_other_d00.021451
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.9353146
X-RAY DIFFRACTIONr_angle_other_deg0.74633612
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1115333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.62826.696115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.35215327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.403156
X-RAY DIFFRACTIONr_chiral_restr0.0990.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022714
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02436
X-RAY DIFFRACTIONr_mcbond_it3.7771.51402
X-RAY DIFFRACTIONr_mcbond_other2.5251.5608
X-RAY DIFFRACTIONr_mcangle_it4.92622273
X-RAY DIFFRACTIONr_scbond_it6.833860
X-RAY DIFFRACTIONr_scangle_it8.274.5835
X-RAY DIFFRACTIONr_rigid_bond_restr4.15733713
X-RAY DIFFRACTIONr_sphericity_free25.5793355
X-RAY DIFFRACTIONr_sphericity_bonded13.5933631
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 600 -
Rwork0.21 5528 -
obs--90.96 %

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