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- PDB-4p6a: Crystal structure of a potent anti-HIV lectin actinohivin in comp... -

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Basic information

Entry
Database: PDB / ID: 4p6a
TitleCrystal structure of a potent anti-HIV lectin actinohivin in complex with alpha-1,2-mannotriose
ComponentsActinohivin
KeywordsSUGAR BINDING 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
Biological speciesActinomycete sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.398 Å
AuthorsZhang, F. / Hoque, M.M. / Suzuki, K. / Tsunoda, M. / Naomi, O. / Tanaka, H. / Takenaka, A.
CitationJournal: Chembiochem / Year: 2014
Title: The characteristic structure of anti-HIV actinohivin in complex with three HMTG D1 chains of HIV-gp120.
Authors: Zhang, F. / Hoque, M.M. / Jiang, J. / Suzuki, K. / Tsunoda, M. / Takeda, Y. / Ito, Y. / Kawai, G. / Tanaka, H. / Takenaka, A.
History
DepositionMar 23, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionMar 4, 2015ID: 4G1S
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 2.0Nov 22, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / diffrn_source ...atom_site / diffrn_source / entity / entity_src_nat / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_validate_symm_contact / software / struct_conn / struct_keywords / struct_site_gen
Item: _atom_site.label_asym_id / _diffrn_source.pdbx_synchrotron_site ..._atom_site.label_asym_id / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _entity_src_nat.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _software.classification / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_keywords.text / _struct_site_gen.label_asym_id
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description / 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_struct_special_symmetry / refine_hist / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _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 / _pdbx_struct_special_symmetry.label_asym_id / _refine_hist.d_res_high / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 3.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 3.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actinohivin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0464
Polymers12,5321
Non-polymers1,5133
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint28 kcal/mol
Surface area5370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.970, 27.230, 56.910
Angle α, β, γ (deg.)90.000, 119.790, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-312-

HOH

21A-358-

HOH

31A-368-

HOH

DetailsMonomer

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Components

#1: Protein Actinohivin


Mass: 12532.492 Da / Num. of mol.: 1 / Fragment: UNP residues 47-160 / 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-(1-2)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1122h-1a_1-5]/1-1-1/a2-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.66 Å3/Da / Density % sol: 53.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 3% PEG400, 0.1 M sodium/potassium phosphate, pH 6.2, 0.8 M ammonium sulfate

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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 210r / Detector: CCD / Date: May 26, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.398→49.389 Å / Num. all: 25397 / Num. obs: 25397 / % possible obs: 96.3 % / Redundancy: 3.7 % / Rpim(I) all: 0.052 / Rrim(I) all: 0.1 / Rsym value: 0.086 / Net I/av σ(I): 4.312 / Net I/σ(I): 10.7 / Num. measured all: 95140
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.398-1.473.80.18141341735710.1080.1815.994.1
1.47-1.563.80.1544.51319734850.0910.1547.195.7
1.56-1.673.80.1265.11230232620.0750.1268.796.1
1.67-1.83.80.1085.61155430710.0650.10810.396.3
1.8-1.983.70.0936.21072728660.0560.09311.997.4
1.98-2.213.70.0856.4965325940.0510.08513.398.2
2.21-2.553.70.0836.7858422990.050.0831497.7
2.55-3.133.80.0835.8736819580.050.0831598.4
3.13-4.423.70.0747.6554115110.0450.07415.797.1
4.42-21.6763.60.0727.727977800.0440.07215.290

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
RefinementResolution: 1.398→21.69 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.679 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1692 2556 10.1 %RANDOM
Rwork0.1408 22840 --
obs0.1437 25396 95.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.63 Å2 / Biso mean: 12.875 Å2 / Biso min: 4.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0 Å2-0.11 Å2
2--0.64 Å20 Å2
3----0.19 Å2
Refinement stepCycle: final / Resolution: 1.398→21.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms886 0 204 174 1264
Biso mean--19.64 29.82 -
Num. residues----114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021125
X-RAY DIFFRACTIONr_bond_other_d0.0010.02919
X-RAY DIFFRACTIONr_angle_refined_deg2.2352.1381560
X-RAY DIFFRACTIONr_angle_other_deg0.9093.0022152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2745113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.0224.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.78715122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.797156
X-RAY DIFFRACTIONr_chiral_restr0.1130.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021118
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02248
LS refinement shellResolution: 1.398→1.434 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 182 -
Rwork0.18 1619 -
all-1801 -
obs--91.7 %

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