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- PDB-2ds2: Crystal structure of mabinlin II -

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Basic information

Entry
Database: PDB / ID: 2ds2
TitleCrystal structure of mabinlin II
Components
  • Sweet protein mabinlin-2 chain ASweetness
  • Sweet protein mabinlin-2 chain BSweetness
KeywordsPLANT PROTEIN / SEED STORAGE PROTEIN / SWEET PROTEIN
Function / homology
Function and homology information


nutrient reservoir activity
Similarity search - Function
AAI/SS protein, conserved domain / Napin/ 2S seed storage protein/Conglutin / Plant lipid-transfer and hydrophobic proteins / Hydrophobic Seed Protein / Protease inhibitor/seed storage/LTP family / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETIC ACID / Sweet protein mabinlin-2
Similarity search - Component
Biological speciesCapparis masaikai (plant)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 1.7 Å
AuthorsLi, D.F. / Zhu, D.Y. / Wang, D.C.
CitationJournal: J.Struct.Biol. / Year: 2008
Title: Crystal structure of Mabinlin II: a novel structural type of sweet proteins and the main structural basis for its sweetness.
Authors: Li, D.F. / Jiang, P. / Zhu, D.Y. / Hu, Y. / Max, M. / Wang, D.C.
History
DepositionJun 19, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sweet protein mabinlin-2 chain A
B: Sweet protein mabinlin-2 chain B
C: Sweet protein mabinlin-2 chain A
D: Sweet protein mabinlin-2 chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0655
Polymers25,0054
Non-polymers601
Water2,252125
1
A: Sweet protein mabinlin-2 chain A
B: Sweet protein mabinlin-2 chain B


Theoretical massNumber of molelcules
Total (without water)12,5032
Polymers12,5032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-16 kcal/mol
Surface area5450 Å2
MethodPISA
2
C: Sweet protein mabinlin-2 chain A
D: Sweet protein mabinlin-2 chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5633
Polymers12,5032
Non-polymers601
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-16 kcal/mol
Surface area5820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.110, 51.080, 47.340
Angle α, β, γ (deg.)90.00, 122.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide Sweet protein mabinlin-2 chain A / Sweetness / Mabinlin II / MAB II


Mass: 4174.806 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Capparis masaikai (plant) / Tissue: SEED / References: UniProt: P30233
#2: Protein Sweet protein mabinlin-2 chain B / Sweetness / Mabinlin II / MAB II


Mass: 8327.779 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Capparis masaikai (plant) / Tissue: SEED / References: UniProt: P30233
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 1.6 Å3/Da / Density % sol: 24.5 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: SODIUM MALONATE, SODIUM ACETATE , pH 4.60, VAPOR DIFFUSION, HANGING DROP, temperature 310K

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Data collection

DiffractionMean temperature: 83 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 25, 2005
RadiationMonochromator: CON-FOCUSE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→20.5 Å / Num. obs: 17686 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 6
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.266 / % possible all: 100

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Processing

Software
NameVersionClassification
CRYSTALCLEARdata collection
SCALAdata scaling
SHARPphasing
CNS1.1refinement
CrystalCleardata reduction
RefinementMethod to determine structure: SIRAS / Resolution: 1.7→20.35 Å / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1641 -RANDOM
Rwork0.221 ---
obs0.221 16657 93.6 %-
all-17686 --
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.7→20.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1547 0 0 129 1676
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.8
X-RAY DIFFRACTIONc_improper_angle_d0.97
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.029
RfactorNum. reflection% reflection
Rfree0.434 230 -
Rwork0.374 --
obs--77.2 %

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