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- PDB-3hp8: Crystal structure of a designed Cyanovirin-N homolog lectin; LKAM... -

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Basic information

Entry
Database: PDB / ID: 3hp8
TitleCrystal structure of a designed Cyanovirin-N homolog lectin; LKAMG, bound to sucrose
ComponentsCyanovirin-N-like protein
KeywordsSUGAR BINDING PROTEIN / Cyanovirin-N / CVNH / lectin / carbohydrate / sucrose
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
HIV-inactivating Protein, Cyanovirin-n / Cyanovirin-N / Cyanovirin-N / Cyanovirin-N superfamily / CVNH domain / CVNH / Roll / Mainly Beta
Similarity search - Domain/homology
sucrose / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Cyanovirin-N homolog / Cyanovirin-N homolog
Similarity search - Component
Biological speciesTuber borchii (whitish truffle)
Neurospora crassa (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKoharudin, L.M.I. / Furey, W. / Gronenborn, A.M.
Citation
Journal: Proteins / Year: 2009
Title: A designed chimeric cyanovirin-N homolog lectin: Structure and molecular basis of sucrose binding.
Authors: Koharudin, L.M. / Furey, W. / Gronenborn, A.M.
#1: Journal: Structure / Year: 2008
Title: The Evolutionarily Conserved Family of Cyanovirin-N Homologs: Structures and Carbohydrate Specificity
Authors: Koharudin, L.M.I. / Viscomi, A.R. / Jee, J.G. / Ottonello, S. / Gronenborn, A.M.
History
DepositionJun 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / 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.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_assembly_gen.asym_id_list / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 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: Cyanovirin-N-like protein
B: Cyanovirin-N-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4518
Polymers24,7732
Non-polymers1,6786
Water4,360242
1
A: Cyanovirin-N-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2254
Polymers12,3861
Non-polymers8393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cyanovirin-N-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2254
Polymers12,3861
Non-polymers8393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.497, 39.298, 86.134
Angle α, β, γ (deg.)90.00, 97.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cyanovirin-N-like protein


Mass: 12386.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tuber borchii (whitish truffle), (gene. exp.) Neurospora crassa (fungus)
Plasmid: pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5MK11, UniProt: Q7S6U4
#2: Polysaccharide
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 3.01 Å3/Da / Density % sol: 59.18 %
Crystal growTemperature: 277 K / pH: 8
Details: protein solutions (~40 mg/ml) were incubated overnight with sucrose at a molar ratio of 1:40 (protein:disaccharide) and crystallization were carried out using 0.2 M Li2SO4, 0.1 M Tris-HCl ...Details: protein solutions (~40 mg/ml) were incubated overnight with sucrose at a molar ratio of 1:40 (protein:disaccharide) and crystallization were carried out using 0.2 M Li2SO4, 0.1 M Tris-HCl (pH 8.5), and 30% PEG 4000 with protein to mother liquor ratio of 8 to 1 , VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 10, 2007
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.88→35.7 Å / Num. obs: 23572 / % possible obs: 96.7 % / Observed criterion σ(I): 3 / Redundancy: 3.08 % / Rmerge(I) obs: 0.166 / Net I/σ(I): 3.9
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 2.92 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 1.4 / % possible all: 76.1

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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: 3HNU

3hnu


Resolution: 2→35.7 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.905 / SU B: 4.761 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1022 5.1 %RANDOM
Rwork0.224 ---
obs0.227 19030 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-2.26 Å2
2---1.64 Å20 Å2
3---1.02 Å2
Refinement stepCycle: LAST / Resolution: 2→35.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1717 0 108 242 2067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211857
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.982525
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7665216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.0924.054111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82715280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9721522
X-RAY DIFFRACTIONr_chiral_restr0.1150.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021428
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.151.51066
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.87321701
X-RAY DIFFRACTIONr_scbond_it3.2573791
X-RAY DIFFRACTIONr_scangle_it4.8584.5824
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 78 -
Rwork0.245 1434 -
obs--100 %

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