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Entry
Database: PDB / ID: 4den
TitleStructural insightsinto potent, specific anti-HIV property of actinohivin; Crystal structure of actinohivin in complex with alpha(1-2) mannobiose moiety of high-mannose type glycan of gp120
ComponentsActinohivin
KeywordsANTIVIRAL PROTEIN / anti-HIV lectin / molecular recognition / high-mannose type glycan
Function / homology
Function and homology information


regulation of defense response to virus / carbohydrate binding
Similarity search - Function
Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
2alpha-alpha-mannobiose / : / Actinohivin
Similarity search - Component
Biological speciesActinomycete (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHoque, M.M. / Suzuki, K. / Tsunoda, M. / Jiang, J. / Zhang, F. / Takahashi, A. / Naomi, O. / Zhang, X. / Sekiguchi, T. / Tanaka, H. ...Hoque, M.M. / Suzuki, K. / Tsunoda, M. / Jiang, J. / Zhang, F. / Takahashi, A. / Naomi, O. / Zhang, X. / Sekiguchi, T. / Tanaka, H. / Omura, S. / Takenaka, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structural insights into the specific anti-HIV property of actinohivin: structure of its complex with the alpha(1–2)mannobiose moiety of gp120
Authors: Hoque, M.M. / Suzuki, K. / Tsunoda, M. / Jiang, J. / Zhang, F. / Takahashi, A. / Ohbayashi, N. / Zhang, X. / Tanaka, H. / Omura, S. / Takenaka, A.
History
DepositionJan 20, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_symm_contact / struct_conn / struct_conn_type / 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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_seq_id_1
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...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
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: Actinohivin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6777
Polymers12,5321
Non-polymers1,1446
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.217, 56.217, 56.217
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-204-

K

21A-205-

K

31A-307-

HOH

41A-315-

HOH

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Components

#1: Protein Actinohivin


Mass: 12532.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Actinomycete (bacteria) / Strain: K97-0003 / References: UniProt: Q9KWN0
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose / 2alpha-alpha-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 2alpha-alpha-mannobiose
DescriptorTypeProgram
DManpa1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][a-D-Manp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 20% w/v PEG 1000, 0.2M NaCl, 0.1M Na/K phosphate buffer pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→39.75 Å / Num. obs: 8067 / % possible obs: 99.5 % / Redundancy: 19.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 19.3 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 7.8 / Num. unique all: 402 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A07

3a07


Resolution: 1.6→39.75 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.928 / SU B: 1.914 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE CRYSTAL HABIT SHOWS THE SPACE GROUP TO BE P213 APPARENTLY AT THE HIGHEST CONFIDENCE. IN THE CRYSTAL STRUCTURE, HOWEVER, AUTHORS HAVE FOUND THAT THREE ACTINOHIVIN MOLECULES (IN COMPLEX ...Details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
RfactorNum. reflection% reflectionSelection details
Rfree0.20167 370 4.6 %RANDOM
Rwork0.14473 ---
obs0.14721 7647 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.958 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms875 0 72 69 1016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021970
X-RAY DIFFRACTIONr_angle_refined_deg2.1972.0031332
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7285111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.19924.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24615121
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.212156
X-RAY DIFFRACTIONr_chiral_restr0.1530.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021739
X-RAY DIFFRACTIONr_mcbond_it1.1761.5547
X-RAY DIFFRACTIONr_mcangle_it1.8092870
X-RAY DIFFRACTIONr_scbond_it2.9223423
X-RAY DIFFRACTIONr_scangle_it3.7794.5462
LS refinement shellResolution: 1.598→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 25 -
Rwork0.197 554 -
obs-554 100 %

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