2DS2

Crystal structure of mabinlin II

> Summary

Summary for 2DS2

DescriptorSweet protein mabinlin-2 chain A, Sweet protein mabinlin-2 chain B
Functional Keywordsplant protein, seed storage protein, sweet protein
Biological sourceCapparis masaikai
Total number of polymer chains4
Total molecular weight25065.41
Authors
Li, D.F.,Zhu, D.Y.,Wang, D.C. (deposition date: 2006-06-19, release date: 2007-06-12, modification date: 2008-11-04)
Primary citation
Li, D.F.,Jiang, P.,Zhu, D.Y.,Hu, Y.,Max, M.,Wang, D.C.
Crystal structure of Mabinlin II: a novel structural type of sweet proteins and the main structural basis for its sweetness.
J.Struct.Biol., 162:50-62, 2008
PubMed: 18308584
DOI: 10.1016/j.jsb.2007.12.007
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.7 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.261180.6%2.5%18.0%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 2ds2
no rotation
Molmil generated image of 2ds2
rotated about x axis by 90°
Molmil generated image of 2ds2
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 2ds2
no rotation
Molmil generated image of 2ds2
rotated about x axis by 90°
Molmil generated image of 2ds2
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (2ds2.pdb1.gz [17.97 KB])
Coordinate files for Biological unit (2ds2.pdb2.gz [18.45 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, CSweet protein mabinlin-2 chain Apolymer334174.82
UniProt (P30233)
Capparis masaikaiMabinlin II, MAB II
B, DSweet protein mabinlin-2 chain Bpolymer728327.82
UniProt (P30233)
Capparis masaikaiMabinlin II, MAB II
ACETIC ACIDnon-polymer60.11
waterwater18.0125

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains4
Total molecular weight25005.4
Non-Polymers*Number of molecules1
Total molecular weight60.1
All*Total molecular weight25065.4
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.7 Å)
Cell axes80.11051.08047.340
Cell angles90.00122.7790.00
SpacegroupC 1 2 1
Resolution limits20.35 - 1.70
the highest resolution shell value1.810 - 1.700
R-factor0.221
R-work0.22100
the highest resolution shell value0.374
R-free0.25400
the highest resolution shell value0.434
RMSD bond length0.005
RMSD bond angle1.200

Data Collection Statistics

Resolution limits20.50 - 1.70
the highest resolution shell value -
Number of reflections17686
Rmerge_l_obs0.053
the highest resolution shell value0.266
Completeness99.5
Redundancy3.6
the highest resolution shell value3.5
I/sigma(I)0

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP4.6310

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0045735molecular_functionnutrient reservoir activity
C0045735molecular_functionnutrient reservoir activity
B0045735molecular_functionnutrient reservoir activity
D0045735molecular_functionnutrient reservoir activity
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC15BINDING SITE FOR RESIDUE ACY D 1001
ChainResidue
CARG24
DARG27
DPHE49
DPHE69
DARG70

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
ACY_2ds2_D_10016ACETIC ACID binding site
ChainResidueligand
DARG27ACY: ACETIC ACID
DGLN31ACY: ACETIC ACID
DPHE49ACY: ACETIC ACID
DPRO68-ARG70ACY: ACETIC ACID

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails
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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb2ds2.ent.gz (38.36 KB)
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all (no-compress)pdb2ds2.ent (164.29 KB)
header onlypdb2ds2.ent.gz (4.82 KB)
Display
PDBx/mmCIF2ds2.cif.gz (48.39 KB)
PDBMLall2ds2.xml.gz (72.24 KB)
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no-atom2ds2-noatom.xml.gz (14.21 KB)
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ext-atom2ds2-extatom.xml.gz (39.5 KB)
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PDBMLplusall2ds2-plus.xml.gz (73.54 KB)
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no-atom2ds2-plus-noatom.xml.gz (15.52 KB)
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add only2ds2-add.xml.gz (1.3 KB)
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RDF2ds2.rdf.gz (27.91 KB)
Display
Structure factorsr2ds2sf.ent.gz (245.1 KB)
Biological unit (PDB format)2ds2.pdb1.gz (17.97 KB) (A,B)
*author and software defined assembly, 2 molecule(s) (dimeric)
Display
2ds2.pdb2.gz (18.45 KB) (C,D)
*author and software defined assembly, 2 molecule(s) (dimeric)
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Validation reportsPDF2ds2​_validation.pdf.gz (288.82 KB)
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PDF-full2ds2​_full​_validation.pdf.gz (297.37 KB)
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XML2ds2​_validation.xml.gz (12.4 KB)
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PNG2ds2​_multipercentile​_validation.png.gz (157.75 KB)
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SVG2ds2​_multipercentile​_validation.svg.gz (946 B)
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Sequence (fasta)2ds2​_seq.txt
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