5GVY

Crystal structure of SALT protein from Oryza sativa

> Summary

Summary for 5GVY

DescriptorSalt stress-induced protein, ALPHA-D-MANNOSE (3 entities in total)
Functional Keywordssalt tolerance, rice, mannose binding lectin, sugar binding protein
Biological sourceOryza sativa subsp. indica (Rice)
Total number of polymer chains2
Total molecular weight30780.4
Authors
Sharma, P.,Sagar, A.,Kaur, N.,Sharma, I.,Kirat, K.,Ashish, F.N.U.,Pati, P.K. (deposition date: 2016-09-07, release date: 2017-09-13)
Primary citation
Sharma, P.,Sagar, A.,Kaur, N.,Sharma, I.,Kirat, K.,Ashish, FNU.,Pati, P.K.
Crystal structure of SALT protein from Oryza sativa
To Be Published,
Experimental method
X-RAY DIFFRACTION (1.662 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.201501.3%1.7%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5gvy
no rotation
Molmil generated image of 5gvy
rotated about x axis by 90°
Molmil generated image of 5gvy
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BSalt stress-induced proteinpolymer14515210.02
UniProt (A2WPN7)
Pfam (PF01419)
Oryza sativa subsp. indica (Rice)Salt protein,Protein lectin-like,Protein mannose-binding lectin
ALPHA-D-MANNOSEnon-polymer180.22
waterwater18.0418

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight30420.1
Non-Polymers*Number of molecules2
Total molecular weight360.3
All*Total molecular weight30780.4
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.662 Å)

Cell axes48.29158.81151.558
Cell angles90.00114.3990.00
SpacegroupP 1 21 1
Resolution limits25.56 - 1.66
the highest resolution shell value1.715 - 1.662
R-factor0.1641
R-work0.16210
the highest resolution shell value0.189
R-free0.20050
the highest resolution shell value0.234
RMSD bond length0.007
RMSD bond angle0.912

Data Collection Statistics

Resolution limits50.00 - 1.66
the highest resolution shell value -
Number of reflections31076
Rmerge_l_obs0.033
the highest resolution shell value0.134
Completeness97.4
Redundancy2.5
the highest resolution shell value1.9
I/sigma(I)2

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, SITTING DROP8-9291

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
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC110binding site for residue MAN A 201
ChainResidue
AGLY13
AGLY14
AGLY133
ATHR134
ALEU135
AASP137
AHOH312
AHOH363
AHOH438
AHOH441

AC210binding site for residue MAN B 201
ChainResidue
BGLY13
BGLY14
BLEU88
BGLY133
BTHR134
BLEU135
BASP137
BHOH303
BHOH365
BHOH379

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

site_idNumber of ResiduesDetails
MAN_5gvy_A_20110ALPHA-D-MANNOSE binding site
ChainResidueligand
AGLY13-GLY14MAN: ALPHA-D-MANNOSE
ALEU88MAN: ALPHA-D-MANNOSE
AILE91MAN: ALPHA-D-MANNOSE
ASER132-ASP137MAN: ALPHA-D-MANNOSE

MAN_5gvy_B_20110ALPHA-D-MANNOSE binding site
ChainResidueligand
BGLY13-GLY14MAN: ALPHA-D-MANNOSE
BLEU88MAN: ALPHA-D-MANNOSE
BILE91MAN: ALPHA-D-MANNOSE
BSER132-ASP137MAN: ALPHA-D-MANNOSE

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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

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