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- PDB-2dpf: Crystal Structure of curculin1 homodimer -

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Basic information

Entry
Database: PDB / ID: 2dpf
TitleCrystal Structure of curculin1 homodimer
ComponentsCurculin
KeywordsPLANT PROTEIN / sweet taste / taste modifying
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
Biological speciesCurculigo latifolia (lumbah)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKurimoto, E. / Suzuki, M. / Amemiya, E. / Yamaguchi, Y. / Nirasawa, S. / Shimba, N. / Xu, N. / Kashiwagi, T. / Kawai, M. / Suzuki, E. / Kato, K.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Curculin Exhibits Sweet-tasting and Taste-modifying Activities through Its Distinct Molecular Surfaces.
Authors: Kurimoto, E. / Suzuki, M. / Amemiya, E. / Yamaguchi, Y. / Nirasawa, S. / Shimba, N. / Xu, N. / Kashiwagi, T. / Kawai, M. / Suzuki, E. / Kato, K.
History
DepositionMay 11, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Curculin
B: Curculin
C: Curculin
D: Curculin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1857
Polymers50,8974
Non-polymers2883
Water10,305572
1
A: Curculin
B: Curculin


Theoretical massNumber of molelcules
Total (without water)25,4492
Polymers25,4492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-25 kcal/mol
Surface area10980 Å2
MethodPISA, PQS
2
C: Curculin
D: Curculin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7375
Polymers25,4492
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-57 kcal/mol
Surface area11040 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)51.996, 54.249, 84.055
Angle α, β, γ (deg.)90.00, 104.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Curculin


Mass: 12724.265 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Curculigo latifolia (lumbah) / Plasmid: PET22B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19667
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 572 / 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: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3
Details: 5% PEG 8000, 0.25M lithium sulfate, 0.1M citrate , pH 3.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.827 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.827 Å / Relative weight: 1
ReflectionResolution: 1.4→40 Å / Num. all: 87424 / Num. obs: 87424 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.55 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.3
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 2.21 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.4 / Num. unique all: 8176 / % possible all: 92

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KJ1

1kj1


Resolution: 1.5→38.85 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1048961.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 7203 10.1 %RANDOM
Rwork0.221 ---
obs0.221 71543 98.3 %-
all-71543 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.4395 Å2 / ksol: 0.356083 e/Å3
Displacement parametersBiso mean: 23.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.75 Å20 Å2-3.02 Å2
2--0.5 Å20 Å2
3----4.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.5→38.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3464 0 15 572 4051
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.314 1235 10.3 %
Rwork0.293 10749 -
obs-10749 99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4so4_xplor_paramso4_xplor_top

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