2DS2

Crystal structure of mabinlin II

> Summary

Summary for 2DS2

DescriptorSweet protein mabinlin-2 chain A, Sweet protein mabinlin-2 chain B, ACETIC ACID, ... (4 entities in total)
Functional Keywordsplant protein, seed storage protein, sweet protein
Biological sourceCapparis masaikai
Total number of polymer chains4
Total molecular weight25065.22
Authors
Li, D.F.,Zhu, D.Y.,Wang, D.C. (deposition date: 2006-06-19, release date: 2007-06-12, Last modification date: 2011-07-13)
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 (PDB entries with the same primary citation)
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%17.5%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 weight25005.2
Non-Polymers*Number of molecules1
Total molecular weight60.1
All*Total molecular weight25065.2
*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

> 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 (47.94 KB)
PDBMLall2ds2.xml.gz (63.3 KB)
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no-atom2ds2-noatom.xml.gz (13.02 KB)
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ext-atom2ds2-extatom.xml.gz (37.43 KB)
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PDBMLplusall2ds2-plus.xml.gz (64.61 KB)
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no-atom2ds2-plus-noatom.xml.gz (14.33 KB)
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add only2ds2-add.xml.gz (1.31 KB)
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RDF2ds2.rdf.gz (26.52 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 (452.64 KB)
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PDF-full2ds2​_full​_validation.pdf.gz (460.45 KB)
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XML2ds2​_validation.xml.gz (11.29 KB)
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PNG2ds2​_multipercentile​_validation.png.gz (146.95 KB)
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SVG2ds2​_multipercentile​_validation.svg.gz (948 B)
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Sequence (fasta)2ds2​_seq.txt
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