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- PDB-3s5x: Structure of the cyanobacterial Oscillatoria Agardhii Agglutinin ... -

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Basic information

Entry
Database: PDB / ID: 3s5x
TitleStructure of the cyanobacterial Oscillatoria Agardhii Agglutinin (OAA) in complex with a3,a6 mannopentaose
ComponentsLectin
KeywordsPROTEIN BINDING / BETA BARREL LIKE PROTEIN / 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
alpha-D-mannopyranose / Lectin / Lectin OAA
Similarity search - Component
Biological speciesPlanktothrix agardhii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 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 1.3Oct 29, 2014Group: Structure summary
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7555
Polymers14,0621
Non-polymers1,6934
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.192, 49.070, 69.247
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: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a1122h-1b_1-5][a1122h-1a_1-5]/1-2-2-2/a3-b1_a6-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.13 Å3/Da / Density % sol: 42.14 %
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) with protein and 3,6-mannopentaose at molar ratios of 1:2, 1:3, or 1:4 (the protein concentration kept at 40 mg/ml), 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: Jul 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: 1.65→35.19 Å / Num. all: 13024 / Num. obs: 13024 / % possible obs: 96.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2 / Redundancy: 12.02 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 27.5
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 8.91 % / Rmerge(I) obs: 0.118 / Mean I/σ(I) obs: 13.2 / % possible all: 87.4

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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: 1.65→35.19 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.847 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21874 1460 10.1 %RANDOM
Rwork0.17765 ---
obs0.18156 13024 96.51 %-
all-13024 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.374 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å2-0 Å2
2--1 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.65→35.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms983 0 112 126 1221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211141
X-RAY DIFFRACTIONr_angle_refined_deg1.5322.0191566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2075141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.01626.48154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.91115145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.753153
X-RAY DIFFRACTIONr_chiral_restr0.10.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021843
X-RAY DIFFRACTIONr_mcbond_it0.7951.5655
X-RAY DIFFRACTIONr_mcangle_it1.34521039
X-RAY DIFFRACTIONr_scbond_it1.8953486
X-RAY DIFFRACTIONr_scangle_it2.6154.5522
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 82 -
Rwork0.231 847 -
obs--85.23 %

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