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- PDB-2d04: Crystal structure of neoculin, a sweet protein with taste-modifyi... -

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Basic information

Entry
Database: PDB / ID: 2d04
TitleCrystal structure of neoculin, a sweet protein with taste-modifying activity.
Components
  • Curculin
  • neoculin acidic subunit
KeywordsPLANT PROTEIN / all beta
Function / homology
Function and homology information


response to other organism / carbohydrate binding
Similarity search - Function
Agglutinin, subunit A / Bulb-type lectin domain / Bulb-type lectin domain / Bulb-type lectin domain superfamily / Bulb-type lectin domain profile. / Bulb-type mannose-specific lectin / Orthogonal Prism / Mainly Beta
Similarity search - Domain/homology
: / Curculin-1 / Curculin-2
Similarity search - Component
Biological speciesCurculigo latifolia (lumbah)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsShimizu-Ibuka, A. / Morita, Y. / Terada, T. / Asakura, T. / Nakajima, K. / Iwata, S. / Misaka, T. / Sorimachi, H. / Arai, S. / Abe, K.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal structure of neoculin: insights into its sweetness and taste-modifying activity
Authors: Shimizu-Ibuka, A. / Morita, Y. / Terada, T. / Asakura, T. / Nakajima, K. / Iwata, S. / Misaka, T. / Sorimachi, H. / Arai, S. / Abe, K.
History
DepositionJul 25, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_biol / struct_conn / 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.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 25, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 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: neoculin acidic subunit
B: Curculin
C: neoculin acidic subunit
D: Curculin
E: neoculin acidic subunit
F: Curculin
G: neoculin acidic subunit
H: Curculin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,96110
Polymers100,0078
Non-polymers9542
Water2,972165
1
A: neoculin acidic subunit
B: Curculin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2233
Polymers25,0022
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-21 kcal/mol
Surface area10660 Å2
MethodPISA
2
C: neoculin acidic subunit
D: Curculin


Theoretical massNumber of molelcules
Total (without water)25,0022
Polymers25,0022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-28 kcal/mol
Surface area10550 Å2
MethodPISA
3
E: neoculin acidic subunit
F: Curculin


Theoretical massNumber of molelcules
Total (without water)25,0022
Polymers25,0022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-25 kcal/mol
Surface area10390 Å2
MethodPISA
4
G: neoculin acidic subunit
H: Curculin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7353
Polymers25,0022
Non-polymers7331
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-15 kcal/mol
Surface area11160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.009, 101.089, 271.572
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a heterodimer and four heterodimer is included in the asymmetric unit.

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Components

#1: Protein
neoculin acidic subunit


Mass: 12408.771 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Curculigo latifolia (lumbah) / References: GenBank: 50344707, UniProt: Q6F495*PLUS
#2: Protein
Curculin / Neoculin basic subunit


Mass: 12593.067 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Curculigo latifolia (lumbah) / References: UniProt: P19667
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3) ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpb1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5][a1122h-1b_1-5]/1-2-1-3/a3-b1_a4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 3.3 Å3/Da / Density % sol: 62.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG1000, sodium cacodylate, calcium chrolide, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 16, 2004
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.76→50 Å / Num. all: 32626 / Num. obs: 32626 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.76→2.86 Å / % possible all: 82.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERV. 1.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BWU

1bwu


Resolution: 2.76→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1973203.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 3246 10 %RANDOM
Rwork0.245 ---
obs0.245 32517 92.8 %-
all-32517 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 11.5444 Å2 / ksol: 0.331918 e/Å3
Displacement parametersBiso mean: 31.5 Å2
Baniso -1Baniso -2Baniso -3
1--9.09 Å20 Å20 Å2
2--14.33 Å20 Å2
3----5.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.76→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6884 0 63 165 7112
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d28.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.25
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_scbond_it1.872
X-RAY DIFFRACTIONc_scangle_it2.862.5
LS refinement shellResolution: 2.76→2.93 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.355 433 9.1 %
Rwork0.32 4312 -
obs-4312 82.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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