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- PDB-4g1r: Crystal structure of anti-HIV actinohivin in complex with alphs-1... -

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Basic information

Entry
Database: PDB / ID: 4g1r
TitleCrystal structure of anti-HIV actinohivin in complex with alphs-1,2-mannobiose (Form II)
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 / Actinohivin
Similarity search - Component
Biological speciesActinomycete sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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 alpha-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
DepositionJul 11, 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.src_method / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actinohivin
C: Actinohivin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1198
Polymers25,0652
Non-polymers2,0546
Water4,972276
1
A: Actinohivin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5594
Polymers12,5321
Non-polymers1,0273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Actinohivin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5594
Polymers12,5321
Non-polymers1,0273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.760, 66.860, 66.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11C-415-

HOH

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Components

#1: Protein Actinohivin


Mass: 12532.492 Da / Num. of mol.: 2 / 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.: 6
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 50% MPD, 0.2M Ammonium phosphate monobasic, 0.1M Tris (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: 1.4→12.45 Å / Num. obs: 38564 / % possible obs: 78.7 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 18.8
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.083 / Mean I/σ(I) obs: 5.7 / % possible all: 19.6

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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: 1.57→12.45 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.13 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19409 1689 5.1 %RANDOM
Rwork0.16034 ---
obs0.162 31551 95.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.158 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å2-0 Å20 Å2
2--0.27 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.57→12.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1772 0 138 276 2186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.021962
X-RAY DIFFRACTIONr_bond_other_d0.0010.021664
X-RAY DIFFRACTIONr_angle_refined_deg2.1162.0012694
X-RAY DIFFRACTIONr_angle_other_deg0.9963.0023818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9065226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36224.4100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98715244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6481512
X-RAY DIFFRACTIONr_chiral_restr0.140.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022236
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02496
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4041.51114
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.13421770
X-RAY DIFFRACTIONr_scbond_it2.7733848
X-RAY DIFFRACTIONr_scangle_it3.9914.5924
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.57→1.61 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.172 112 -
Rwork0.163 1763 -
obs--75.45 %

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