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- PDB-4end: Crystal structure of anti-HIV actinohivin in complex with alpha-1... -

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Basic information

Entry
Database: PDB / ID: 4end
TitleCrystal structure of anti-HIV actinohivin in complex with alpha-1,2-mannobiose (P 2 21 21 form)
ComponentsActinohivin
KeywordsANTIVIRAL PROTEIN / Actinohivin / anti-HIV lectin / 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 / ACETONITRILE / Actinohivin
Similarity search - Component
Biological speciesActinomycete sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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: To be Published
Title: Matured structure of anti-HIV lectin actinohivin in complex with 1,2-mannobiose
Authors: 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.
History
DepositionApr 13, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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
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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)13,6416
Polymers12,5321
Non-polymers1,1095
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.840, 66.840, 67.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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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 sp. (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-CCN / ACETONITRILE


Mass: 41.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.49 Å3/Da / Density % sol: 50.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M Ammonium phosphate, 0.1M Tris, 50% (v/v) 2-Methyl-2,4-pentanediol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→27.84 Å / Num. obs: 10409 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 11.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 4.6 / Num. unique all: 1483 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DEN

4den


Resolution: 1.9→25.7 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.907 / SU B: 3.052 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23094 497 4.8 %RANDOM
Rwork0.16382 ---
obs0.16703 9805 99.13 %-
all-10409 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.345 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms886 0 75 144 1105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.021985
X-RAY DIFFRACTIONr_angle_refined_deg1.9082.0031349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4425113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85424.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.76215122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.195156
X-RAY DIFFRACTIONr_chiral_restr0.1440.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021747
X-RAY DIFFRACTIONr_mcbond_it1.1911.5559
X-RAY DIFFRACTIONr_mcangle_it1.9472887
X-RAY DIFFRACTIONr_scbond_it3.1213426
X-RAY DIFFRACTIONr_scangle_it4.4564.5462
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 38 -
Rwork0.209 696 -
obs-696 99.46 %

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